Enzymes 2.5, 8.1.

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Enzymes 2.5, 8.1

Enzymes 2.5 Understanding (Statement objectives) Define enzyme and active site (to which specific substrates bind). State enzyme catalysis involves molecular motion and the collision of substrates with the active site. State temperature, pH and substrate concentration affect the rate of activity of enzymes. State that enzymes can be denatured. State that immobilized enzymes are widely used in industry. Applications Explain the use of lactase in the production of lactose-free milk. Describe methods of production of lactose-free milk and its advantages. Lactase can be immobilized in alginate beads and experiments can then be carried out in which the lactose in milk is hydrolysed. Nature of science Experimental design—State that accurate, quantitative measurements in enzyme experiments require replicates to ensure reliability. Draw and label graphs to show the expected effects of temperature, pH and substrate concentration on the activity of enzymes. Explain patterns and trends in these graphs. Skills (Design of experiments to test) Explain the effects of temperature, pH and substrate concentration on the activity of enzymes. Experimental investigation of a factor affecting enzyme activity. Explain that enzymes lower the activation energy of the chemical reactions that they catalyze. Explain the difference between competitive and noncompetitive inhibition with reference to one example of each. Explain the control of metabolic pathways by end-product inhibition, including the role of allosteric sites.

Enzymes 8.1 Understanding Metabolic pathways consist of chains and cycles of enzyme-catalysed reactions. Enzymes lower the activation energy of the chemical reactions that they catalyse. Enzyme inhibitors can be competitive or non-competitive. Enzyme inhibition should be studied using one specific example for competitive and non-competitive inhibition. Metabolic pathways can be controlled by end-product inhibition. Applications Explain the end-product inhibition of the pathway that converts threonine to isoleucine. Explain the use of databases to identify potential new anti-malarial drugs. Nature of science Developments in scientific research follow improvements in computing—Describe developments in bioinformatics, such as the interrogation of databases, have facilitated research into metabolic pathways. Skills Calculate and plot rates of reaction from raw experimental results. Distinguish different types of inhibition from graphs at specified substrate concentration

Enzymes

Enzymes control cell metabolism Enzymes are: globular proteins biological catalysts that speed up reactions they are not used up in a reaction Lower activation energy of a reaction

Enzyme- Substrate Specificity Enzymes are found in all living cells Living organisms produce many different enzymes Enzymes only catalyse one biochemical reaction- this is called enzyme- substrate specificity The shape and chemical properties of the active site and substrate match each other Substrate can bind, but not other substances

Enzyme-substrate complex Once an enzyme binds with its substrate, it is called an enzyme-substrate complex In order to bind, the substrate must collide with the enzyme Collision theory

Everything you need to know Something more interactive

Manipulating Enzymes Enzymes are important resources for many industries For example: Lactase is used in milk to create lactose-free milk (more on this later) Restriction enzymes used in plasmids to create recombinant DNA Taq polymerase used in PCR reactions

Common uses of enzymes in industry include: Detergents contain proteases and lipases to help breakdown protein and fat stain In the textiles industry enzymes help in the processing of fibres, e.g. polishing cloth to make it appear more shiny Enzymes are used to breakdown the starch in grains into biofuels that can be combusted

Common uses of enzymes in industry include: Enzymes are widely used in the food industry, e.g. fruit juice, pectin to increase the juice yield from fruit Fructose is used as a sweetener, it is converted from glucose by isomerase Rennin is used to help in cheese production

Enzymes used in industry are usually immobilized Enzymes used in industry are usually immobilized. They are attached to a material so that their movement is restricted. Common ways of doing this are: Aggregations of enzymes bonded together Attached to surfaces, e.g. glass Entrapped in gels, e.g. alginate gel beads

Advantages of enzyme immobilization: Concentration of substrate can be increased as the enzyme is not dissolved – this increases the rate of reaction Recycled enzymes can be used many times, immobilized enzymes are easy to separate from the reaction mixture, resulting in a cost saving. o Separation of the products is straight forward (this also means that the the reaction can stopped at the correct time). Stability of the enzyme to changes in temperature and pH is increased reducing the rate of degradation, again resulting in a cost saving.

Production of Lactose-free milk Lactase obtained from commonly from yeast (bacteria is an alternative) Lactase is bound to the surface of alginate beads Milk is passed (repeatedly) over the beads The lactose is broken down into glucose and galactose The immobilized enzyme remains to be used again and does not affect the quality of the lactose free milk

Other uses of lactose free milk: As a means to increase the sweetness of milk (glucose and galactose are sweeter in flavour), thus negating the need for artificial sweeteners As a way of reducing the crystallisation of ice-creams (glucose and galactose are more soluble than lactose) As a means of shortening the production time for yogurts or cheese (bacteria ferment glucose and galactose more readily than lactose)

HIGHER LEVEL

More on activation energy

How do enzymes lower the activation energy of a reaction? The substrate binds to the enzymes’ active site and the active site is altered to reach the transition state. Due to the binding the bonds in the substrate molecule are stressed/become less stable. The binding lowers the overall energy level of the transition state. The activation energy of the reaction is therefore reduced.

Anabolic Reactions small molecules are used as building blocks to create larger ones “Biosynthesis” Two substrates enter a enzyme and chemical bonds are formed to create one macromolecule Require energy to form these bonds endothermic

Catabolic Reactions Catabolic reactions Used to break down larger molecules into smaller subunits Enzyme is used to break one substrate into two Thus chemical bonds are broken, releasing energy exothermic

Examples?

However... Body rarely achieves the required product after just one reaction Thus, metabolic pathways consists of chains and cycles of enzyme-catalysed reactions

Metabolic pathways

End-Product Inhibition End-product inhibition prevents the cell from wasting chemical resources and energy by making more of a product than it needs Metabolic reactions occur in an assembly line fashion to reach a specific end product

End-Product Inhibition Once there is enough end-product, the whole metabolic pathway shuts down The end-product binds to the very first enzyme allosterically As the end-product is used up, the enzyme is reactivated In high concentrations, the end-product inhibits. In low concentrations, no inhibition.

Glycolysis, a part of respiration, is an example of a metabolic chain Examples Glycolysis, a part of respiration, is an example of a metabolic chain The Calvin cycle, a part of photosynthesis, is an example of a metabolic cycle

Enzyme inhibitors can be competitive or non-competitive. http://www.northland.cc.mn.us/biology/biology1111/animations/enzyme.swf

Enzyme inhibitors can be competitive or non-competitive.

Enzyme inhibitors can be competitive or non-competitive.

Enzyme inhibitors can be competitive or non-competitive.

Enzyme inhibitors can be competitive or non-competitive.

Features of competitive inhibitors Distinguishing different types of inhibition from graphs at specified substrate concentration. Features of competitive inhibitors Rate of reaction is reduced When the concentration of substrate begins to exceed the amount of inhibitor, the maximum rate of the uninhibited enzyme can be achieved. However, it takes a much higher concentration of substrate to achieve this maximum rate. https://wikispaces.psu.edu/download/attachments/46924781/image-6.jpg

Features of non-competitive inhibitors Distinguishing different types of inhibition from graphs at specified substrate concentration. Features of non-competitive inhibitors Rate of reaction is reduced The binding of the non-competitive inhibitor prevents some of the enzymes from being able to react regardless of substrate concentration. Those enzymes that do not bind inhibitors follow the same pattern as the normal enzyme. It takes approximately the same concentration of enzyme to reach the maximum rate, but the maximum rate is lower than the uninhibited enzyme. https://wikispaces.psu.edu/download/attachments/46924781/image-6.jpg

Enzyme inhibitors can be competitive or non-competitive. http://highered.mheducation.com/sites/dl/free/0072437316/120070/bio10.swf

Isoleucine is an essential amino acid* End-product inhibition of the pathway that converts threonine to isoleucine. Isoleucine is an essential amino acid* Bacteria synthesize isoleucine from threonine in a series of five enzyme-catalysed steps As the concentration of isoleucine increases, some of it binds to the allosteric site of threonine deaminase Isoleucine acts as a non-competitive inhibitor to threonine deaminase The pathway is then turned off, regulating isoleucine production. If the concentration of isoleucine later falls (as a result of its use) then the allosteric sites of threonine deaminase are emptied and the enzymes recommences the conversion of threonine to isoleucine takes place. *Essential amino acids cannot be made by the body, therefore they must come from food.

Denaturation Enzymes are proteins, therefore they get denatured as well Denaturation effects both the primary and tertiary structures of an enzyme this causes a loss of shape and change in activation site Once an enzyme has lost its shape, it can no longer bind with its substrate

Temperature Denaturation Rise in heat energy causes atoms of the enzyme to get excited They begin to vibrate, causing the weaker bonds to break Once the bonds break, the activation site is altered, disallowing the substrate from bonding

pH Denaturation H+ will change the electrostatic attraction between two amino acids When pH is altered, H+ concentrations will either increase or decrease, attaching themselves to the enzyme This causes new bonds to form or break Once bonds are altered, the shape of the enzyme is also altered

Use of databases to identify potential new anti-malarial drugs. Bioinformatics is an approach whereby multiple research groups can add information to a database enabling other groups to query the database. Bioinformatics has facilitated research into metabolic pathways is referred to as chemogenomics. Sometimes when a chemical binds to a target site, it can significantly alter metabolic activity. Massive libraries of chemicals are tested individually on a range of related organisms. For each organism a range of target sites are identified. A range of chemicals which are known to work on those sites are tested. http://upload.wikimedia.org/wikipedia/commons/0/02/Mosquito_bite4.jpg

Use of databases to identify potential new anti-malarial drugs. Malaria is a disease caused by the pathogen Plasmodium falciparum. This protozoan uses mosquitoes as a host as well as humans and hence can be passed on by mosquito bites Increasing drug resistance to anti-malarial drugs has lead to the use of bioinformatics and chemogenomics to try and identify new drugs. In one study, approx. 300,000 chemicals were screened against a chloroquine-sensitive 3D7 strain and the chloroquine-resistant K1 strain of P. falciparum. Other related and unrelated organisms, including human cell lines, were also screened. (19) new chemicals that inhibit the enzymes normally targeted by anti-malarial drugs were identified Additionally (15) chemicals that bind to malarial proteins were identified – this can help in the location of P. falciparum These results indicate possible new directions for drug research. http://upload.wikimedia.org/wikipedia/commons/0/02/Mosquito_bite4.jpg

Review...

Environmental effects on rate activity of enymes Three things affect enzyme activity rate Temperature pH Substrate Concentration You need to be able to draw and clearly explain their effects! Simulation

Temperature At low temperatures, very little enzyme activity This is because not enough heat energy present to initiate collision and bond formation As temperature increases, enzyme activity also increases This occurs until temperatures increases to a specific point The enzyme then denatures Thus, enzymes have a narrow temperature in which they function

pH enzymes have an optimal pH Range deviating from optimal is very narrow Too acidic or too basic and the enzyme will begin to denature However, pH within the body varies greatly, so enzymes adapt to suit the pH they operate in Pepsin is an enzyme in the stomach to break down food. Why is it’s optimal pH so low?

Substrate Concentration Enzyme activity increases as substrate concentration increase This is until substrate concentration surpasses enzyme concentration Then, enzyme activity plateaus Why?

What is the effect of substrate concentration? Design of experiments to test the effect of temperature, pH and substrate concentration on the activity of enzymes. Experimental investigation of a factor affecting enzyme activity. (Practical 3) Catalase is one of the most widespread enzymes. It catalyses the conversion of hydrogen peroxide, a toxic by-product of metabolism, into water and oxygen. H2O2 Catalase H2O + O2 Possible research questions, what are you going to investigate (independent variable)? What is the effect of substrate concentration? What is the effect of temperature? What is the effect of pH? Important things to consider: How are you going to vary the mass/volume/concentration of your variable? What units will you be measuring your variable in? Have you chosen an effect range or values to answer your question? Are the concentrations/chemicals you are using safe to handle?

How are you going to measure your results (dependent variable)? Design of experiments to test the effect of temperature, pH and substrate concentration on the activity of enzymes. Experimental investigation of a factor affecting enzyme activity. (Practical 3) How are you going to measure your results (dependent variable)? What equipment will you be using to measure your results? What are the units and uncertainty given both the equipment and how you choose to use it? What time period do you need to run the experiment for? How fast is the enzyme action likely to be? How many repeats will you need to make sure your results are reliable? http://www.scienceexperimentsforkids.us/wp-content/uploads/2011/08/hydrogen-experiments-for-kids-3-img.jpg

How are you going to make sure it is a fair test (control variables)? Design of experiments to test the effect of temperature, pH and substrate concentration on the activity of enzymes. Experimental investigation of a factor affecting enzyme activity. (Practical 3) How are you going to make sure it is a fair test (control variables)? What variables other than your independent variable could affect the results? Why would these variables affect the results? How will you ensure each is kept constant and monitored? What level should they be kept constant at? If a control variable is too far from it’s optimum then it could limit the enzyme action and no change would be seen in the results. If a variable cannot be controlled it should still be discussed and considered as an uncontrolled variable. Safety and ethics: Are you using any equipment that may cause you or others harm? What steps have you taken to minimize this risk?

Calculating and plotting rates of reaction from raw experimental results. http://www.scienceexperimentsforkids.us/wp-content/uploads/2011/08/hydrogen-experiments-for-kids-3-img.jpg

Lab Enzyme catalysis