Enzymes as catalysts
A catalyst is a substance that increases the rate of a chemical reaction but is not changed by side reaction. Because they are not changed by the reactions they can catalyse reactions multiple times so only small amounts of enzymes are needed compared to the quantity of reactant needed.
Platinum is an example of an inorganic catalyst as it is used in the catalytic converters fitted to vehicles with combustion engines to convert unburned hydrocarbons in exhaust gases to carbon dioxide and water.
Enzymes are biological catalysts they are made by living cells to speed up biochemical reactions in these reactions enzymes convert substrate into products meaning that substrate plus enzyme equals product.
Role of enzymes in metabolism
Metabolism is the complex network of independent and interacting chemical reactions that occur in living organisms. Many of these reactions happen inside cells but there are also some extra cellular reactions for example the digestion of food in the intestine.
There are thousands of metabolic reactions and they form pathways in which one type of molecule is transformed into another by a series of small steps. Most of these pathways are chains of reaction, but there are also some cycles.
Enzymes give living organisms considerable control over their medical metabolism and therefore over their activities and chemical composition.
Enzyme specificity
Almost all metabolic reactions are catalyse by an enzyme. One of the priorities of enzymes is their specificity. Each enzyme catalyse one specific reaction or a specific group of reactions, this is a significant difference between enzymes and non-biological catalysts such as planum which can catalyse many different reactions. Because of enzyme specificity living organisms can make large numbers of different enzymes.
Enzyme specificity has many benefits it allows organisms to control metabolism. If a cell produces an enzyme, it can drive a particular reaction that would otherwise happen extremely slowly or not at all. By making more or less of an enzyme cells can control the rate of a reaction there are also mechanisms for temporarily stopping particular enzymes from working a reaction is not required for a while.
Anabolic reactions
Metabolism has two parts anabolism and catabolism. Anabolic reactions build up smaller molecules into larger ones. These reactions require energy. Photosynthesis is an example of anabolism because carbon dioxide, water and other small molecules are combined to produce larger molecules, using energy from light. In anabolic reactions macro molecules are produced from monomers using energy from ATP. They are condensation reactions because water is a byproduct example examples of anabolic reactions include
-protein synthesis (translation) by ribosomes
-dna synthesis (replication)
-Synthesis of complex carbohydrates, including starch cellulose and glycogen.
Catabolic reactions
Metabolism has two parts anabolism and catabolism. Catabolic reactions breakdown larger molecules into smaller ones releasing energy in some cases this energy is captured by coupling the catabolic reaction to the synthesis of ATP which can then be used in the cell examples of catabolic reactions include:
-Digestion of food -in humans this happens in the mouth, stomach and small intestine
-Cell respiration - in aerobic respiration glucose and lipids are oxidised to carbon dioxide and water
-Digestion of complex carbon compound- decomposers do this with dead organic matter
Enzymes as globular proteins with an active site
Enzymes are globular proteins with precise three-dimensional structure and chemical properties that allow them to function as catalysts. For a reaction to be catalysed the substrate or substrate must bind to a special region on the surface of the enzyme called the active site. The shape and chemical properties of the active site and the substrate match each other. This allows the substrate to bind with the enzyme while most other substances cannot. While the substrate is bound to the active site it is converted into products. The products are then released leaving the active site free to catalyse another reaction.
Active sites very in size, depending the size of the substrate. Typically just a few amino acids at the active site are essential to create the chemical conditions that change the substrate enough to convert them into products. After the amino acids that formed the active site are not next to each other in the polypeptide that make up the enzyme they are brought together by the folding of the polypeptide for that reason the overall three-dimensional structure of the enzyme is crucial. If any part of the enzyme is altered, the structure of the active site may change and the catalysis is unlikely to happen.
Enzyme substrate binding
Interactions between the substrate and the active site of an enzyme are the bases of catalysis. A substrate approaches the active site until it is near the enzyme. The substrate’s direction of movement is random when it is close enough to interact the chemical properties of the enzyme surface attract the substrate molecule towards the active site.
The substrate binds to the active site and this used to be compared with a key fitting into a lock however that model is inappropriate because interactions between the substrate and the active site cause both to change bond angles and bond lengths are altered changing the three-dimensional molecular shapes of the substrate and active site this is called induced fit binding.
If there is a second substrate, it approaches and binds to another part of the active site again the substrate and the active site cause changes in each other to allow binding. Changes to the substrate molecules make it easier for bonds within them to break and for new bonds to form converting substrate into products. The products then detach from the active site. Without substrate or products interacting with it the enzymes active site returns to its original state. It is now empty and available for those substrates to buy so the catalytic cycle can be repeated..
Substrate active site collision in enzyme catalysis
A substrate molecule can only bind for the active side of an enzyme if it moves very close to it this can happen as a result of molecular motion. When a substrate and an active site come together, this is known as substrate-active site collision. This collision is similar to molecular motion in liquids.
In a liquid your molecules are packed closely together but they are free to move. The direction of each molecule changes repeatedly and at random if the liquid contains both substrate and enzyme molecules they will occasionally come together. The rate at which this happens will increase if there is a higher concentration of substrate or enzyme molecules or if the temperature increases leading to faster molecular motion.
One collision occurs the substrate may be at any angle to the active site. Successful collisions are ones in which the substrate and active site are aligned so binding can take place. Some enzymes have chemical properties that draw substrate towards the active site or adjust their orientation however the forces involved only work over short distances so they can only promote binding when a subject molecule is already very close to the active site .
There were some variation in the molecular motion of substrate and enzymes :
- Many enzyme catalyse reactions happen in the cytoplasm. Substrate and enzyme are both dissolved in water so they are free to move. In most cases however the substrate is a smaller molecule than the enzyme so it moves more.
-Some substrates are very large and do not move much in these cases the enzyme has to move in relation to the substrate enzymes that replicate or transcribe DNA do this.
-Some enzymes are embedded in membranes and cannot move. They are immobilised in these cases the substrate has to do all the movement.
Enzyme-substrate specificity
The shape and chemical properties of an enzymes active site allows substrate molecules to bind to it but not other substances. This is called enzyme-substrate specificity.
Some enzymes are absolutely specific and always bind to the same substrate for example glucose is the only substrate that finds the active site of the enzyme glucokinase but hexokinase can bind to anyone of a group of hexose sugars.
Denaturation
Enzymes are proteins with a precise three-dimensional shape and an intricate chemical structure. This structure depends on relatively weak interactions between amino acids within the protein including hydrophobic and hydrogen bonds. These interactions are affected by factors such as heat and acidity so enzymes are easily altered. Even if changes happen at a distance from the active site interactions within the enzyme are likely to affect the active site. Even small changes to the active site can prevent binding to substrate or prevent catalysis after binding. As a result, the enzyme will no longer work as a catalyst if the changes are too great to be reversed the enzyme will be denatured.
Effects of temperature on the rate of enzyme activity
And activity is affected by temperature in two ways. In liquids the particles are in continual random motion. When a liquid is heated, the particles gain kinetic energy so as a result the enzyme substrate molecules move around more quickly and the chance of a substrate molecule colliding with the active site of the enzyme is increased therefore enzyme activity is increased.
When enzymes are heated bonds in the enzyme vibrate more the chance of these bonds breaking is increased. When bonds in the enzyme break the enzyme structure changes. Changes to the active site will mean it could no longer bind with substrate molecules so the enzyme becomes denatured and enzyme activity will fall. Different enzyme molecules denature at slightly different temperatures. once enzymes are denatured completely catalysis will stop completely.
Effects of pH on the rate of enzyme activity
Enzymes are sensitive to their chemical environment in particular they are affected by how acidic or alkaline it is. Acidity is due to the presence of hydrogen ions (protons). The higher the hydrogen ion concentration the more acidic a solution is. The pH scale is a measure of hydrogen ion concentration and therefore acidity. A lower pH value indicates a higher hydrogen ion concentration and therefore greater acidity.
The pH scale is logarithmic and a solution at pH seven is neutral.
Most enzymes have an optimum pH at which their activity is highest. If pH increases or decreases from the optimum ionic bonds between the amino acids in the enzyme are altered. This changes the structure of the enzyme, including it active site. As a result, the active site will no longer bind to substrate or convert them into products. On a certain pH, the enzyme will be in reversibly denatured.
Not all enzymes have the same optimum pH in fact there is a wide range. This reflects the varied environment in which enzymes work.
Effect of substrate concentration on the rate of enzyme activity
Enzymes cannot catalyse a reaction until the substrate binds with the active site. Collisions between substrates and active sites occur due to random movements of molecules and liquids. If the concentration of substrate molecules is increased. Substrate active site collision will occur more frequently and the rate at which the enzyme catalyse its reaction will increase.
However, there is another trend that affects the rate of reaction once a substrate has bound to an active site, the active site is occupied and unavailable to other substrate molecules until products have been informed and released. As the substrate concentration rises more, more active sites are occupied at any moment therefore a greater proportion of substrate active site collisions are blocked. For this reason the increases in the rate at which enzymes catalyse reactions get smaller and smaller as substrate concentration rises.
variables (enzyme experiment)
-Independent variables are factors that are being investigated, so they are deliberately varied to see what the effect is. Often there is just one independent variable making data from the experiment easy to analyse. Variables are independent if the researcher has a free choice of what levels to use. An enzyme experiments the independent variable is commonly temperature, substrate concentration, enzyme concentration or pH.
-Control variables are factors that must be kept at a constant to ensure the experiment is a “fair test”. Control variables should be monitored regularly to ensure they do not change. In a properly designed and some experiment, all factors that could affect and some activity apart from the independent variable are control variables.
-lastly the dependent variables are the results of the experiments. In an enzyme experiment the dependent variable is the quantity that is measured to calculate the reaction rate. Only changes to the independent variable should affect the level of the dependent variable. This rate is often called enzyme activity.
Reaction rate calculations
Calculations of reaction rates is an important skill whether you do this using data from your own experiment or secondary data from an experiment carried out by someone else. Reaction time is the speed at which substrates are converted to products so the units are the change in the amount of chemical divided by time, for example millimoles per second. There are two approaches to finding the reaction time:
- Allow the reaction to happen for a fixed time and measure the amount of substrate used up or product form. The time should be relatively short so the substrate concentration remains high.
- Start with a known amount of substrate and allow for reactions to continue until all the substrate has been converted to products measure the time taken for the reaction to go to completion.
With both approaches the quantity of product or substrate is divided by the time.
Activation energy
Chemical reactions are not a single step process. Substrates have to pass through a transition state before they are converted into products. Energy is required to reach this transition state. This is called activation energy and is used to breakdown bonds in substrate molecules. Energy is also released as a new bond is made And as the product is formed.
A reaction is exothermic when there is a net release of energy. The energy released as a new bonds is made greater than the activation energy needed to break bonds and reached the transition state.
When this reaction is catalysed by an enzyme the net amount of energy released is the same but the activation energy is smaller. This is because the bonds of the substrate or weakened is it bound to the active site, so less energy is needed to break them. As a result, the rate of the reaction increases typically by a factor of 1 million or more .
Intracellular and extracellular enzyme catalysed reactions
Enzymes are synthesised by ribosomes. Extracellular enzymes are released from the cell and work outside it. They are synthesised by ribosomes attached to the endoplasmic reticulum. Intracellular enzymes for use inside of the cell are synthesis by free ribosomes in the cytoplasm.
Intracellular enzymes catalyse metabolic pathways such as glycolysis. The first reaction glycolysis is the addition of a phosphate group to the glucose molecule. This reaction is catalysed by the enzyme hexokinase in the cytoplasm. Some intracellular enzymes work inside organelles.
Many extracellular enzymes catalyse the breakdown of larger macro molecules. The monomer is produced and then pass through the plasma membrane and enter cells. For humans and other multicellular organisms this process occurs in the digestive system were solid food is digested by extracellular enzymes.
Unicellular heterotrophic Archea, bacteria and fungi cannot take in macro molecules because their cell walls form a barrier so they cannot perform endocytosis. To feed on macro molecules, these microorganisms secrete extra cellular enzymes. These enzymes work outside the cell to convert the macro molecules into monomer, which can then be absorbed across the plasma membrane.
Generation of heat energy by the reactions of metabolism
The conversion of energy from one form to another is never fully efficient. For example in metabolic reactions the products contain less energy than the reactants therefore the additional energy is converted to heat.
Birds and mammals use the heat generated by metabolism to maintain a body temperature that is greater than that of their environment. Sometimes metabolism releases more heat than is needed for this purpose for example during exercise the human body produces sweat and uses evaporative cooling to dissipate excess metabolic heat.
Metabolic pathways
Cells can perform a huge range of chemical reactions and have thousands of different types of enzymes to do this. Most enzyme catalyse reactions cause a small change in the substrate large chemical transformations happen not in one large jump the sequence of small steps. Together these steps form a metabolic pathway.
Most metabolic pathways involve a chain of reactions for example glycolysis which involves nine different chemical reactions.
Branching of metabolic pathways is very common and metabolism as a whole is a network of interlinked and interdependent pathways.
Cycle of reactions
Cycles of reactions are similar to metabolic pathways just more unusual. In a cycle every intermediate is a product of one reaction and a substrate of another reaction. Two examples of this is the Calvin cycle and the Krebs cycle
Allosteric sites and non-competitive inhibition
Every enzyme has an active site, to which the substrate binds. Many enzymes have a second active site where a different specific substance can bind and unbind. Binding and unbinding from this site causes the enzyme to change shape, this site is called the allosteric site.
Allosteric sites on enzymes have evolved because they allow the activity of an enzyme to be regulated. Switching between the two alternative states alters the structure and properties of the enzymes active site. In some cases, binding to the steric site activates an enzyme so it will catalyse a reaction . In other cases binding prevents catalysts and the enzyme is reversibly inhibited. Substances that inhibit an enzyme by binding to the steric site rather than the active site do not compete with substrate so they are known as non-competitive inhibitors.
Competitive inhibition
Competitive enzyme inhibitors bind to the active site of an enzyme. As long as the inhibitor remains bound, the substrate cannot bind and the enzyme cannot catalyse its reaction. Competitive inhibitors are structurally similar to the substrate so they combine to the same active site however unlike the substrate they are not converted into products and so remain bound for longer than the substrate.
When the active site of an enzyme is vacant either a substrate or an inhibitor molecule combined. Whichever molecule arrives first and binds successfully with the active site will be the winner in the competition. The extent of inhibition becomes greater if the concentration of the competitive inhibitor increases.
If the inhibitor concentration is relatively low and the sub concentration is increased, the extent of inhibition will reduce until the enzyme is effectively uninhibited. With many more substrate molecules than inhibitor molecules substrate almost always arrive at the active site first. This is not the case with non-competitive inhibitors because increases in substrate concentration cannot prevent a non-competitive inhibitor from binding to the allosteric site.
End product inhibition
The complex network of metabolic pathways in a cell must be regulated to ensure they produce enough of each substance but not too much many pathways are controlled by a feedback inhibition system. In the system is the product of the last reaction the pathway inhibits the first reaction from occurring again.
The enzyme that is inhibited has an steric site to which the end product Bynes. This binding changes the shape of the steric site preventing catalysis for as long as the end product remains bound. This is an example of a non-competitive inhibition and also of negative feedback. If too much of the end product is made it will increasingly inhibit the first enzyme in the pathway. This effectively switches off the whole pathway and prevents synthesis of more and product.
Irreversible binding of an inhibitor/mechanism based inhibition
Some inhibitions can be irreversible. Heavy metals such as mercury and lead are non-specific inhibitors of a wide range of enzymes because they bind irreversibly to -SH groups in the amino acid cysteine wherever it occurs in the structure of an enzyme. For this reason these heavy metals are very toxic if they enter the body and they are dangerous pollutant of the environment.
Some irreversible inhibitors target one specific enzyme such inhibitors are structurally similar to the substrate so they bind to the enzymes active site. Once these irreversible inhibitors bind to the active site they become permanently bound by the formation of a covalent bond. This produces a stable inhibitor and enzyme complex and the enzyme can never work as a catalyst again and this is called mechanism based inhibition.
Mechanism based inhibitors can cause harm to an organism because every molecule of the inhibitor can permanently inactivate one enzyme molecule, the inhibitor may kill an organism if the function of the inhibited enzyme is vital and there is a lethal concentration of the inhibitor. Some living organism synthesise a mechanism based enzyme inhibitor in order to kill another organism for example, penicillin.
