BIOL 1000 Lecture Notes - Lecture 1: Reaction Rate, Protease, Enzyme
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Enzyme Kinetics Simulation Experiment
Adapted from Junker, M. J. Chem. Educ. 2010, 87, 294-295.
Objective:
To simulate the working of enzymes in the catalysis of biochemical reactions.
Materials:
Bolts (15) and nuts to match, purchased at a hardware store or found in your basement. If you donât have any nuts and bolts, use anything made of two parts that can be taken apart. For example, red and blue paper clips, large and small paper clips, baby food jars and lids. Use your imagination. In addition, you will need something to glue the two pieces together. You will also need a device to time yourself, a watch with a second hand or a stop watch.
Background Information and Theory:
Read pp. 655-672 in Seager and Slabaugh. Most of the metabolic reactions in Chapters 23 and 24 are catalyzed by enzymes. Enzymes work by lowering the activation energy for biochemical reactions. The first step is for the substrate (S), the reactant to react with the enzyme (E) to form the Enzyme-Substrate Complex (ES):
E + S ES. The second step is for the enzyme to convert the substrate into the product(s). In this case there will be two products, P1 and P2: ES P1 + P2. In this simulation the substrate will be the nut and bolt screwed together. You will be the enzyme. As the enzyme, it will be your job to find the substrate and unscrew the nut from the bolt. The nut will be P1 and the bolt will be P2. The simulation will simulate the case where the substrate concentration is less than saturation. (Figure 20.6, p. 663), below maximum velocity). It will also simulate saturating the substrate concentration. (Figure 20.6, p. 663, at maximum velocity). Competitive Inhibition, (p. 668) and non-competitive inhibition (p. 669) will be simulated as well.
Procedure:
Enzyme Kinetics When Substrate Concentration is Less Than Saturation
Screw the 15 nuts on to the 15 bolts. Scatter the bolts randomly around the room you are in. Start the timer and gather and unscrew as many nuts as possible in 30 seconds. Record the number of bolts unscrewed on the table/report sheet in Doc Sharing. (I have also placed the table following the write-up on the main page, here. Divide the number of bolts unscrewed by the time (0.5 minutes) to get the rate of the reaction.
Enzyme Kinetics When Substrate is at Saturation
Reattach the 15 nuts to the bolts. Put all the nut/bolt combinations in front of you on the table. Start the timer and unscrew as many nuts as possible in 30 seconds. Record the number of bolts unscrewed on the report sheet. Divide the number of bolts unscrewed by the time (0.5 minutes) to get the reaction rate.
Enzyme Kinetics With Competitive Inhibition
Reattach the nuts to the bolts. Glue 10 of the nuts to the bolts, so they canât be removed. Place the nut/bolt combinations in a pile. Unscrew as many of the nuts as possible in 30 seconds. Count the number of unscrewed nuts. Donât try to muscle the glued ones. They canât be removed. Count the number of nuts unscrewed. Record this number in the table. Also record the reaction rate by dividing by the time (0.5 minutes)
Enzyme Kinetics With Non-Competitive Inhibition
Reattach the nuts to the bolts. Place the nut/bolt combinations in front of you on the table. Have someone tie your hands behind your back, or mentally tie your hands behind your back. Start the timer and see how many nuts you can remove from the bolts. Record the numbers of nuts removed, and divide by time (0.5 minutes) to get the reaction rate.
Fill out table below.
Condition | Number of Bolts Unscrewed | Time (minutes) | Reaction rate (bolts per minute) | Comment |
Scattered bolts | Non-saturated substrate | |||
Pile of Bolts | Saturated Substrate | |||
Some Bolts Glued | Competitive Inhibiter | |||
Arms tied | Non-Competitive Inhibitor |
Answer these questions:
How well do you think this simulation represents enzyme kinetics? Did it help you understand kinetics better? Can you think of anything that could be added to improve the simulation?
Enzyme Activity
1. Briefly explain the principle of spectrophotometry.
2. Which of the following statements is true about enzymes?(check all correct answers)
__ enzymes act on (are specific for) one or just a fewsubstrates | ||
__ enzymes can be denatured (loose their tertiary/quaternarystructure and activity) by extreme conditions such as heat, high orlow pH,or presence of organic solvents | ||
__most enzymes are DNA | ||
__ enzymes are protein | ||
__enzymes perform best at specific conditions of temperature, pHand salt concentration 5. Which enzymes break the following macromolecules? Match the following with their correponding answers: ___ Nucleic acids A. proteases or proteinases such as pepsin ___ Cellulose B. none ___ Triglycerides C. lipases ___ Proteins D. amylases ___ Starch E. nucleases 6.Match the following enzymes totheir products. Answers ___ pepsin, trypsin and other digestive proteases A.Nucleotides ___ salivary and pancreatic amylases and other enzymes B. AminoAcids ___ lipases C. Monosaccharides ___ nucleases D. fatty acids and glycerol 7. Based on experiments, what is the effect of extremeconditions of pH and temperature (boiling tube) on enzymeactivity? 8. ATP stores energy in the form of___ ___ Chemical energy ___ Kinetic energy ___ Thermal energy ___ Activation energy 9. An allosteric site in anenzyme is____ __ the site where reactions occur __ the site that binds aregulator __ the site that binds thesubstrate __ the site that binds the product 10. Enzymes increase the rate of reactions by making thetransition state less stable. __ False 11. Enzymes increase the rate of reactions by placing reactingparts of the molecule in favorable positions. 12. Which of the followingis a mechanism for regulation of enzymes? 13. Which of the following represents a correct order of eventsin an enzyme catalytic cycle? 1.enzyme changes shape 2.substrate binds to active site 3.substrate is converted to products 4. products are released from activesite __ 1>2>3>4 __ 2>1>3>4 __ 3>2>1>4 __ 2>4>3>1 |