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Note On AS Level Biology Enzymes

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Published in: Biology
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AS level Biology Enzymes

Areesha A / Dubai

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Qualification: IGCSE-AS Level-A level

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  1. rood and Row emymes break dogn inb Enzymes
  2. WELCOME ENZYME SCHOOL ALUMNI Poor Jerry... I told him working in non—ideal pH levels would denature him.
  3. L.O — To explore the nature of Enzymes • Success criteria- • To state enzymes functions inside cells and outside cells. • To explain lock and key hypothesis • To explain the mode of action of enzymes— Induced fit hypothesis
  4. Starter • Find the odd one out: Starch Amylase Maltase Maltose
  5. Enzymes Inhibitors Functions Factors that affect enzyme's activity Mode of action Comparing enzyme affinities
  6. Types Of Enzymes Intracellular enzymes Extracellular enzymes • • • • Operates with in the cell. occur in the cytoplasm, organelles or the nucleus. Examples of intracellular enzyme are DNA polymerase, RNA polymerase and ATP synthetase. Secreted by the cells and catalyse reactions outside the cells. Most digestive enzymes are extracellular enzymes. For example, amylase. Fungi secrete enzyme outside their bodies to digest the substrate on which they are growing.
  7. METABOLISM Catabolism (break down) Anabolism (synthesis)
  8. Metabolism Tor sunace Mar-nose-I-p Mar-nose-ep;..::; Glycolysis exopolysachharides Break down into simpler Catabolism (break down) Threonine crwd•chain acid and H&tidine Cid ism molecules with release of energy
  9. Metabolism r S u naCe I - p M Glycolysis ach harides • Synthesis of complex Ami rw molecules which requires energy. Anabolism (synthesis) 0 acid I ism Ty rosine
  10. What are enzymes?? • Biological catalyst • Speeds up a chemical reaction but remains unchanged at the end. Enzyme changes shape Substrate slightly as substrate binds Substrate entering active site of enzyme Enzyme/substrate Enzym e/products complex complex Products leaving active site Of enzyme
  11. Enzymes • Globular protein • Coiled with hydrophilic R group on the outside of the molecule. • Are soluble • Possess active site Active-site cleft
  12. The active site Hydrophobic hollow or cleft on the enzyme surface. Accepts reactants (substrates and cofactors) Contains amino acids which - bind reactants (substrates and cofactors) - catalyse the reaction Active site Active site
  13. Activation energy & Transition State Energy Transition state barrier b Reactants Activation energy is the minimum energy required to start a chemical reaction Heat is needed! Products Course of reaction
  14. Energy barrier b Reactants Transition state Reactant must reach a high- energy intermediate state called the transition state before the products are formed. Products Course of reaction
  15. We need enzymes to lower down the activation energy without having to increase the heat energy. This is done by holding the substrate in such a way that their molecules can react more easily.
  16. Enzymes reduce activation energy Reactants Catalyzed reaction Uncatalyzed reaction Products Course of reaction 2001 Sinauer Associates, Inc,
  17. Biological catalyst Globular protein Active-site cleft Efficient & Highly specific Enzymes Activity is affected by pH, temperature, substrate concentration and enzyme concentration.
  18. *Enzymes are highly specific in terms of what they act upon and what they do. •This specificity and what the enzyme does is made possible by their structures.
  19. Enzyme changes shape Sub strafe as substrae binds Substrate entering Enzyme's ubstrate En pro duce Produce leaving active site Of enzyme Induced-fit hypothesis active site ot enzyme complex Lock-and-key hypothesis complex Mechanism of enzyme action bstrate active site enzyme bonds in substrate are weakened enzyme-substrate products enzyme
  20. (a) Lock-and-key model A clive site Enzyme (b) Induced-fit model nzyrne-substrate complex Substrates Enzyme Enzyrne (unchanged) Enzyrne Product Product Enzyme-sift' strate complex
  21. (a) model AdiW Site Enzyme Enzyme- One key for one lock One type of substrate only for one type of enzymes (specific) Substrate fits exactly (complementary) to the active site of the enzyme. htt s://www. outube.com/watch?v=V8TOWT 7
  22. (b) Induced-tit model Substrates Enzyme Product • Modified version of lock-and-key hypothesis. • Active site is flexible and is not exactly complementary. • Active sites are slightly changed when the enzymes binds with the substrates. The active sight becomes fully complementary upon binding.
  23. Example: the breakdown of sucrose, catalyzed by sucrase Sucrose Active site Enzyme Glucose Fructose
  24. Enzymatic Reaction The close fit brings the molecules close together and in the correct orientation for reaction to take place. • It causes stressing and distortion of chemical bonds of the substrates. This causes the bonds to break and new bonds to form. This makes it easier for the substrate to be changed into the product and hence, lowering the activation energy needed.
  25. Methods of enzyme catalysis Provide a reaction surface (the active site) Provide a suitable environment (hydrophobic) Bring reactants together Position reactants correctly for reaction Weaken bonds in the reactants Lowering the activation energy for a reaction, Thus dramatically increasing the rate of the reaction.
  26. Substrate: sucrose bonded Substrate binds to together Adve the enzyme forming an enzyme-substrate complex @ •re •wed, enzyme to bmd substrh 3. Binding of substrate and enzyme places stress on the glucose i, fructose bond and the bond breaks
  27. Question time • Name the monomer that makes the active site of the enzyme. Are enzymes an example of globular protein .if yes why?
  28. L.O to explore enzymatic reaction • Success criteria- • To list the factors affecting the rate of enzyme catalyzed reaction. • To explain how various factors affect rate of enzyme reaction. • To investigate the progress of an enzyme- catalysed reaction by measuring rates of formation of products
  29. Recap • Log on to www.socrative.com Use the code KOSHY8535 to do a quick assessment.
  30. Understanding an enzymatic reaction... Investigating ther eat which the substrate is conver e Into the product in an enzyme controlled reaction. • amount of substrate changed • amount of products formed Sucrose
  31. • Catalase is an enzyme found in tissues of most living thing which catalyze the breakdown of 1-120 (hydrogen peroxide) into 1-120 and 02. Volume of 02 collected (cm3) Time (s) •Large volume of 02 collected in the first minute •As the reaction continues, rate of 02 released gradually slows down. •Eventually the reaction stops because all the substrates are broken down
  32. ,017 081 OSI Otl 06 09 ? (.ELLI s•o ttID)Yl? (.UI. 7() (.Ltl. YF) I.(P.IIXO JO OtlIttlO.A
  33. Initial rate of reaction (cm3 02min-1)
  34. Why do scientists measure the initial rate of reaction of enzyme-catalysed reactions? / Initial rate of reaction Independent variable They measure rate at start of reaction before any factors, eg. substrate concentration, have had time to change.
  35. Enzyme pH concentration Factors that affect the rate of reaction Substrate Temperature concentration
  36. • Increasing enzyme concentration increases the rate of the reaction (if substrate is in EXCESS/SUFFICIENT). Increasing enzyme concentration increases the number of active sites available to catalyze the reaction. Enzyme concentration 2x Time of reaction
  37. If substrate in excess... Rate of reaction Enzyme concentration
  38. If NO substrate in excess... Rate of reaction Enzyme concentration
  39. Substrate concentration o o Increasing substrate concentration, maximum plateau is reached. Concentration of catalase remains constant and the 1-120 2 is the independent variable. Substrate concentration
  40. • Increasing temperature will Temperature increase the rate of reaction up to an reaction rate). temperature Increasing temperatu increases E's and S's kinetic energy. E and S collide more often per quantity of time. Form more E-S complex.
  41. raE inueases as for any aåner reaction 10 20 80 optimum falls z/ rapidly about 400 C 40 50 60 mpelaüE IOC)
  42. rate of reaction 4 37 Temperature 95 temperature cent • Temperatures above the optimum cause increasing enzyme molecule vibration, breaking down internal bonds and destroying the active site. The enzymes become denatured (lose its shape and activity).
  43. • Enzymes are sensitive to pH. Operates in a narrow range on pH (either extreme sides will denature.) Pepsin 1 3 Trypsin 9 pH
  44. How does pH affect an enzyme's activity? pH is the measure of the concentration of hydrogen ions in a solution. The lower the pH the higher the concentration of hydrogen ions. Hydrogen ions can interact with the R groups of amino acids, affecting the way in which they bond with each other and therefore affect their 3D structure arrangement. A pH which is very different from the optimum pH can cause denaturation of an enzyme.
  45. Neutral pH SUBSTRATE coo coo NH-a ACTIVE SITE
  46. ow ?? (acidic) SUBSTRATE ???? ?-?? ???? ????? SlTE
  47. High pH (alkaline) SUBSTRATE coo- coo NH2 ACTIVE SITE
  48. Enzymes Functions Factors that affect enzyme's activity Inhibitors Mode of action
  49. Mr. Enzyme, Ms. Substrate and Ms. Inhibitor
  50. Mr. Enzyme, Ms. Substrate and Ms. Inhibitor
  51. Mr. Enzyme, Ms. Substrate and Ms. Inhibitor
  52. Mr. Enzyme, Ms. Substrate and Ms. Inhibitor
  53. Enzyme Inhibitor Inhibitors inhibit the activity of enzymes, reducing the rate of their reactions.
  54. Enzyme Inhibitor
  55. Enzyme Inhibition cc c Inhibitors inhibit the activity of enzymes, reducing the rate of their reactions.
  56. (a) Reaction Substate Active site Enzyme En zyme binds substate En zyme re leases products (b) Inhibition Inhibitor Enzyme Enzyme binds inhibitor Inhibitor competes wifri substate
  57. Enzyme inhibition When an inhibitor... Binds temporarily Binds permanently Binds to the active site • Does NOT bind to the active site
  58. When an inhibitor... Binds temporarily Binds permanently Binds to the active site Enzyme Inhibition • Does NOT bind to the active site Non- Competitive competitive Temporary Temporary (allosteric site) (active site) Permanent (active site) (allosteric)
  59. (i) Competitive inhibitors bind reversibly to the enzyme, preventing the binding of substrate. • On the other hand, binding of substrate prevents binding of the inhibitor. Substrate and inhibitor compete for the enzyme. Competitive Reversible
  60. (a) Reaction Substate Active site Enzyme En zyme binds substate En zyme re leases products (b) Inhibition Inhibitor Enzyme Enzyme binds inhibitor Inhibitor competes wifri substate
  61. C2H602 Poisoning • Ethylene glycol is broken down in the body into oxalic acid (a deadly poison) by the enzyme, alcohol dehydrogenase. • Alcohol (ethanol) acts as a competitive inhibitor for alcohol dehydrogenase.
  62. C2H602 Poisoning • Giving the patient large amounts of alcohol will cause the ethanol to compete with ethylene glycol for the active site of alcohol dehydrogenase. Alcohol is the preferred substrate for alcohol dehydrogenase so when it is present, it binds with the enzyme. After a while, the ethylene glycol is harmlessly excreted.
  63. H H 11-0 enzyme (succinic dehydrogenase) substrate (succinate) Normal reaction product (fumarate). After release the enzyme is free for re-use
  64. substrate competitive inhibitor competition to enter acti Ve site enzyme Competitive inhibition o- inhibited enzyme ves normal enzyme/ substrate complex competitive inhibitor (malonate) resembles substrate in structure. Blocks enzyme from reacting with its normal substrate
  65. • Irreversible inhibition Inhibitor binds irreversibly to the active site Covalent bond formed between the drug and the enzyme Substrate is blocked from the active site Increasing substrate concentration does not reverse inhibition Inhibitor likely to be similar in structure to the substrate
  66. Non-competitive Irreversible (ii) Binds to active site and (permanently). It is irreversible. • Permanently blocks the substrate. • No competition can happen. • E.g.: penicillin antibiotic.
  67. Nerve gas (diisopropylfluorophosphate) DFP, combines with serine (an amino acid) on the active site of the enzyme acetylcholinesterase. This enzyme when inhibited cannot bind to acetylcholine (the substrate). Acetylcholine accumulates. Nerve impulses cannot be stopped Prolonged muscle contraction
  68. (iii) Non competitive (reversible) allosteric inhibitors Active site Active site unrecognisable Induced fit Enzyme Allosteric . site Enzyme Allosteric inhibitor Inhibitor binds reversibly to the allosteric site Intermolecular bonds are formed Induced fit alters the shape of the enzyme Active site is distorted and is not recognised by the substrate Increasing substrate concentration reverse inhibition Inhibitor is not similar in structure to the substrate
  69. Non-competitive Binds to allosteric site temporarily • It is reversible. When the inhibitor's concentration diminished by increasing the concentration of the substrate.
  70. (iii) Non competitive (reversible) allosteric inhibitors 0 Inhibition 0 Enzyme Biosynthetic pathway Feedback control Enzymes with allosteric sites often at start of biosynthetic pathways Enzyme is controlled by the final product of the pathway Final product binds to the allosteric site and switches off enzyme Inhibitor may have a similar structure to the final product
  71. • End product inhibition E.g.: ATP (adenosine triphosphate) that act as an allosteric inhibitor which inhibits biochemical reaction. When ATP level falls, the ATP will leave the allosteric site and cellular respiration continues to take place.
  72. (iv) Non competitive (irreversible) allosteric inhibitors When inhibitor bind to the allosteric site permanently. • Increasing substrate concentration would not reverse the reaction. E.g.: heavy metal ions like mercury and silver ions that can bind to other sites of the enzymes.
  73. Graph showing the comparative effects of the different inhibitors on substrate concentration o no inhibitor competitive inhibitor non-competitive inhibitor irreversible inhibitor Substrate concentration
  74. When a competitive inhibitor is present, the enzyme activity is decreased compared to when no inhibitor is present. As the substrate concentration is increased, the activity eventually becomes the same. • You will notice that the optimum substrate concentration is much higher. With a non-competitive inhibitor, the inhibition is not dependent on the substrate concentration and the effect is similar to an irreversible inhibitor.
  75. L.O- To investigate the effects of substrate concentration and inhibitors on enzyme activity • Success criteria- • To explain that the maximum rate of reaction (Vmax) is used to derive the Michaelis-Menten constant (Km) • To explain the effect of immobilising an enzyme in alginate • To carryout mathematical calculations to find Vmax and Km.
  76. Starter • Go to www.SOCRATlVE.COM . Log in Use the code KOSHY8535 to answer the MCQ questions
  77. The effect of substrate concentration on enzyme activity (A) At low concentration of substrate, there is a steep increase in the rate of reaction with increasing substrate concentration. The catalytic site of the enzyme is empty, waiting for substrate to bind, for much of the time, and the rate at which product can be formed is limited by the concentration of substrate which is available. (B) As the concentration of substrate increases, the enzyme becomes saturated with substrate. As soon as the catalytic site is empty, more substrate is available to bind and undergo reaction. The rate of formation of product now depends on the activity of the enzyme itself, and adding more substrate will not affect the rate of the reaction to any significant effect. substrate concertration
  78. Vmax and Km The rate of reaction when the enzyme is saturated with substrate is the maximum rate of reaction, Vmax. x The relationship between rate of reaction concentration of substrate depends on the affinity of the enzyme for its substrate. This is usually expressed as the Km (Michaelis constant) % Vmax Km is the concentration of substrate which permits the enzyme to achieve half Vmax. An enzyme with a high Km has a low affinity for its substrate, and requires a greater concentration of substrate to achieve Vmax. a low Km means only a small amount of substrate is needed to saturate the enzymes - high affinity. ubstrate concentraton
  79. Significance of Vmax and Km values • Helps scientists make computerized models of biochemical pathways or even the behaviour of whoe cells by predicting how each reaction in a proposed pathway will proceed, and therefore how enzymes interact, and then the consequences of changing factors such as pH and temperature can be built into models. By understanding what affects enzyme efficiency, scientists in the future may be able to design better catalysts, which is linked to genetic engineering. • Knowing the Km means we can calculate active sites occupied by substrates for any substrate concentration. We can compare performances of different enzymes.
  80. •It is impossible to find the Vmax by reading results from a graph, because in reality there isn't an infinite substrate concentration. •However, since l/infinity = 0, which can be plotted, Vmax can be found by plotting I/[S] (inverse substrate concentration) on the x-axis and l/velocity (inverse rate). This is called a double reciprocal plot. 2 1/Vmax
  81. •Vmax: On the double reciprocal graph, you can find 1/Vmax on the y- axis. To find Vmax, you can calculate it like this (let's pretend that 1/Vmax is 20 in this example): •1/Vmax = 20 20 x Vmax Vmax = 1/20 Vmax = 0.05 •Km: On the double reciprocal graph, you can find -1/Km on the x-axis. To find the Km, you can calculate it like this (let's pretend -1/Km is -10 in this example): .-1/Km = -10 1=-10 x Km Km = -1/-10 Km = 1/10 0.1 2 1 IVmax
  82. Inhibitions omnetiit.ive • When a substance reduces the rate of activity of the enzyme by competing with the substrate in binding with the enzyme's active sit. Increasing the concentration of the substrate can reduce the degree of inhibition • Non-competitive inhibition: When a substance reduces the rate of activity of an enzyme, but increasing the concentration of substrate does not reduce the degree of inhibition. Such inhibitors may bind to other areas of the enzymes that are not active sites
  83. • • Immo i IZ1ng nzymes Enzymes is immobilized for commercial purpose Lactase is used with milk to produce lactose-free milk Lactase mixed with sodium alginate — then each droplet put into calcium chloride — which then immediately forms beads. These beads are arran ed and milk is oured throu h it
  84. Enzyme immobilisation • Advantages: • Can be reused. Milk does not contain enzyme. Milk containing lactose Alginate beads with immobilised lactase The immobilised lactase converts lactose into glucose and galactose as the milk flows through free milk
  85. Practice time

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