Lab 4 Enzymes online Fall2020 PDF

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Lab 4_Enzymes_online Fall2020...

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Harper College Bio110—Introduction to Biology and Society Lab 4: Enzymes Name: ______________________________________________ Date: ___________ Objectives:  Describe the function of enzymes  Distinguish between hydrolysis reactions and dehydration synthesis reactions  Describe an enzyme’s active site and factors that affect enzyme specificity  Explain how temperature, pH and the concentration of substrates affects enzyme activity Introduction: The ability of living organisms to easily and rapidly carry out chemical reactions, which under ordinary conditions occur very slowly, is because of their ability to produce organic catalysts called enzymes. When we say that an enzyme is a ‘catalyst’ we mean that the enzyme increases the speed of a chemical reaction. Enzymes are very powerful in their catalytic action. They are effective in minute amounts because they are not used up in the reactions they catalyze and therefore can be used repeatedly. Most enzymes are very specific in the reactions they affect. The reactant molecules that enzymes bind to are called substrates. By binding to substrates, enzymes help to drive the chemical reactions that will change them into one or more products. As an example, lactose is a disaccharide found in milk. The digestion (or breakdown) of lactose into smaller monosaccharides is driven by the enzyme lactase. In this case, lactose acts as the substrate for the enzyme lactase; the enzyme lactase is specific to lactose and does not act other sugars. You may be familiar with the genetic condition called lactose intolerance. Individuals with this condition do not make the enzyme lactase, and therefore, these individuals can’t break down lactose. This causes unpleasant digestion, so most people who are lactose intolerant do not enjoy consuming foods with high lactose contents (i.e. dairy products which are rich in lactose sugars). A chemical reaction showing the digestion of lactose using lactase is shown in Figure 1.

Figure 1: Lactase Digestion of Lactose

The enzyme (lactase) catalyzes the reaction that breaks down the substrate (lactose) into the smaller monosaccharides of glucose and galactose (products). Please note that this reaction is reversible. Also note, lactase ends in the suffix ‘-ase’; the names of many enzymes end in this same suffix. Lipase, which helps to break down lipids, and salivary amylase, which helps to break down starch, are two examples. 1

Exercise 1: Overview of enzymes and Metabolic reactions Metabolism is the full set of chemical reactions that occur in the cell. This includes reactions that build large molecules by combining many small molecules as well as reactions that break down large molecules into many small molecules. Small molecules that can be used as building blocks are called monomers, while larger molecules assembled by combining many monomers are called polymers. Enzymes are linked to a cell’s metabolism, because enzymes help to drive these chemical reactions. A. Background on enzymes Go to the “Enzymatic” activity at: https://biomanbio.com/HTML5GamesandLabs/LifeChemgames/enzymatichtml5page.html 

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Click on “Start a New Game!” When asked whether you are using a touchscreen device, select “NO!” Select “Tap or Click Here!” to read some background information about this simulation. Click on “Tap or Click Here” again to advance to the main menu. Click “What are Enzymes?” and follow the instructions on the screen while also answering the questions below. You can advance by clicking “OK” and go back by pressing the small blue arrow in the top left corner. 1. What is an enzyme?

2. Define the term metabolism.

3. What is a hydrolysis reaction? What does a hydrolysis reaction do?

4. Fill in the blank: “Mono” means __________, “Di” means _________, and “Poly” means ___________________. 5. Fill in the blank: When only two monomers are attached together, we can call that molecule a _____________. 6. What is a dehydration synthesis (condensation) reaction? What does this reaction do?

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Play the game using enzymes. Your goal is to get all the Snurfles (fuzzy yellow creatures) on the left to safety on the right side of the screen, while keeping predators (green snakes) from getting to safety on the right. Click on the appropriate enzyme you want to use, then quickly click on the individual monomers you want to link together to form a bridge. To break down a bridge, click on the appropriate enzyme and click on the parts of the polymer-bridge you would like to break down. 2

7. Which enzyme (the one for dehydration synthesis or the one for hydrolysis) was used to form a long polymer-bridge?

8. Which enzyme (the one for dehydration synthesis or hydrolysis) was used to break down the polymer bridge into its monomer units?

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At the end of the game, click on “Jump to Mini-Quiz” and complete the mini-quiz. 9. Are enzymes proteins, nucleic acids, carbohydrates or lipids?

10. Are enzymes needed for metabolism?

11. What are the monomers that make up enzymes called (lipids, nucleic acids, sugars or amino acids)?

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Once you have completed the mini-quiz, you should have been taken back to the main menu for this simulation. Stay on that main menu, as it will be needed for later exercises.

B. Enzyme Specificity Each enzyme can only act on specific substrate molecules to drive chemical reactions. The simulation below should help to explain why. 

Click on “Specificity” in the Enzymatic main menu and follow the instructions on the screen while also answering the questions below. You can advance by clicking “OK” and go back by pressing the small blue arrow in the top left corner. 12. Why is it that each enzyme can only catalyze a very specific chemical reaction?

13. Fill in the blank: The active site of an enzyme can only fit a specific ___________________.

14. Fill in the blank: The end result of the chemical reaction is the ____________________.

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To play the enzyme specificity game, observe the shape of the substrate that is falling. Click on the enzyme that is appropriate for that substrate, then use your arrow keys on your keyboard to move that enzyme left and right until it is positioned so that the substrate falls into the active site. 3

15. How did you pick the correct enzyme for the substrate that was falling?

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At the end of the game, click on “Jump to Mini-Quiz” and complete the mini-quiz. 16. Fill in the blank: The ____________ is the part of the enzyme that binds to the substrate and causes the reaction to occur. 17. Fill in the blank: The _____________ is the substance or molecule that enters the active site and undergoes a chemical reaction. 18. What does enzyme specificity refer to?

19. What is the most important factor in determining the specificity of an enzyme?

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Once you have completed the mini-quiz, you should have been taken back to the main menu for this simulation. Stay on that main menu, as it will be needed for later exercises.

Exercise 2: Factors that affect enzyme activity Several factors can influence enzyme activity, or the rate at which an enzyme can drive a chemical reaction to produce a product. Two factors that can influence activity are the amount of enzyme available as well as salinity. There are additional factors that can influence enzyme activity, which you will examine in this exercise. A. Effect of Temperature on Enzyme Activity  Click on “Experiments” in the Enzymatic main menu and follow the instructions on the screen while also answering the questions below. You can advance by clicking “OK” and go back by pressing the small blue arrow in the top left corner. 20. What three factors can affect the rate at which an enzyme catalyzes a chemical reaction?

21. You will start by examining how temperature affects enzyme activity. Make a hypothesis about how temperature will affect the enzyme reaction rate below.

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22. In this experiment, you are manipulating temperature to measure how the reaction rate of an enzyme is affected. What is the independent variable in this experiment?

23. What is the dependent variable in this experiment?

24. When you first start dragging the slider to increase the temperature, does this increase, decrease, or have no effect on the rate of the reaction?

25. As you drag the slider to increase temperature, what happens to the movement speed of the substrate?

26. Drag the slider to the hottest temperature in the experiment, how has the reaction rate of the enzyme changed?

27. What does it mean if your enzyme is “denatured”?

28. Drag the slider back to a low temperature. Does the enzyme remain denatured or is it able to fold back to its original shape?

29. Was your hypothesis supported? Remember, in science it is okay if your hypothesis isn’t supported, it just means that you need to go back and revise your hypothesis and test it again.

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Click on “Next Concept.” 30. What is meant by “optimal temperature”?

31. Find the peak on the graph, which represents the fastest reaction rate. What is the optimal temperature for the enzyme being examined?

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Click on “Next Concept” and take the Mini-Quiz.

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32. True or False: Substrates (molecules) move faster at higher temperatures.

33. True or False: Faster moving substrates collide with the enzyme more, causing the reaction rate to increase until the optimal temperature is reached.

34. True or False: Hotter temperatures always result in faster reaction rates.

35. Why does the reaction rate slow down drastically when the temperature is too high?

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Stay on the page entitled “Enzymes and pH” once you have finished the mini-quiz.

B. Effect of pH on Enzyme Activity  Read the introductory information about enzymes and pH. 36. You will start by examining how pH affects enzyme activity. Make a hypothesis about how pH will affect the enzyme reaction rate below.

37. In this experiment, you will manipulate pH to measure how the reaction rate of an enzyme is affected. What is the independent variable in this experiment?

38. What is the dependent variable?

39. Slowly drag the slider towards the lowest pH. What happens to the enzyme by the time you reach the lowest pH?

40. Slowly drag the slider toward the original, middle-range pH (around pH 7). Can the denaturation of this enzyme be reversed?

41. Thought question: Can returning back to optimal pH always refold all enzymes?

42. Slowly drag the slider towards the highest pH. What happens to the enzyme before you reach the highest pH?

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43. Was your hypothesis supported? Again, it is okay if it wasn’t supported—this is why we do experiments to test them!

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Click “Next Challenge” and answer the questions in the mini-quiz. 44. True or False: Substrates move faster at higher pH levels.

45. True or False: Above or below the optimal pH, the enzyme becomes less effective.

46. True or False: The optimal pH for ALL enzymes is a pH of 7.

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Stay on the page entitled “Enzymes and Substrate Concentration” once you have finished the mini-quiz.

C. Effect of Substrate Concentration on Enzyme Activity

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Read the introductory information about substrate concentration and pH. 47. What does substrate concentration refer to?

48. You will start by examining how substrate concentration affects enzyme activity. Make a hypothesis about how substrate concentration will affect the enzyme reaction rate below.

49. In this experiment, you will manipulate substrate concentration to measure how the reaction rate of an enzyme is affected. What is the independent variable in this experiment?

50. What is the dependent variable?

51. When you first start to slowly drag the slider to increase substrate concentration, does it increase, decrease or have no effect on the enzyme reaction rate?

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52. What do you see happening to the number of substrate molecules on the screen as the substrate concentration is increased?

53. After you drag the slider to the highest substrate concentration possible for this experiment, describe how substrate concentration affects enzyme reaction rate.

54. How is enzyme activity at varying substrate concentrations different from enzyme activity at varying temperature or pH levels?

55. Was your hypothesis supported? It is OK if it was not supported!

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Click “Next Challenge” and take the mini-quiz. 56. TRUE or FALSE: Increasing substrate concentration denatures the enzyme

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Stay on the page entitled “The Enzymatic Machine” once you have finished the mini-quiz.

D. Practice—Putting it all together Now, lets put together all the concepts you should have learned by completing the activities above.

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Click “OK!” to play The Enzymatic Machine game. 57. How did you choose the appropriate enzyme for the given substrate?

58. Using the graph at the right, what is the optimal temperature for this enzyme?

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59. Using the graph below, what is the optimal pH for this enzyme?

60. Using the graph below, what is the optimal substrate concentration for this enzyme?

61. Thinking critically: Observe the product(s) that your enzymatic machine produces. Does this enzyme perform hydrolysis or dehydration synthesis? Why?

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Click “continue” to return to the main menu. You click on the “Quiz” for more practice questions if you wish. The following questions are not directly based on the simulation, so use your knowledge of enzymes to answer them. 62. In some produce items, like potatoes and apples, the enzyme catalase drives a chemical reaction that converts the substrate catechol into the product benzoquinone. Benzoquinone is what makes potatoes and apples turn brown after they have been cut 9

and exposed to oxygen. The optimal pH for the enzyme catalase is pH7 and the optimal temperature for its functioning is 37ºC (98ºF). a. Suggest one way that you could prevent a cut apple from turning brown (i.e. suggest one thing you could do to prevent the formation of benzoquinone). What does this do to the enzyme?

63. DNA polymerase is an enzyme in our cells that takes free nucleotide monomers and uses them to assemble larger DNA molecules. a. Identify the substrate(s) and product(s) for this enzyme

b. Is DNA polymerase performing dehydration synthesis (condensation) or hydrolysis?

64. You’re developing an experiment that examines how alcohol concentration affects enzyme reaction rate. a. Develop a hypothesis for this experiment.

b. Identify the independent and dependent variables in this experiment.

65. What is the optimal pH of the enzyme represented by the graph below?

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