BIOL 2020 Lecture 12: BIOC 2300 - Lecture 12
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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?
QUESTION 10
If you can drink milk as an adult, it means that you have inherited a mutation in the promoter of your lactase gene (the gene that encodes the enzyme you need to break down lactose). Predict the effect of this mutation:
The mutation changes the number of domains in the enzyme, which makes it work more efficiently | ||
The mutation changes the amino acid sequence of the lactase protein | ||
The mutation increases the number of copies of the lactase gene that will be found in your genome | ||
The mutation changes whether the lactase sequence is found in an intron or exon | ||
The mutation affects the expression of the lactase gene |
1.2 points
QUESTION 11
A competitive inhibitor is decreasing the activity of an enzyme. Predict the effect of adding more substrate to the reaction.
The substrate will increase the reaction rate by binding to the allosteric site | ||
The substrate will increase the reaction rate by competing with the inhibitor for the active site | ||
The reaction rate will not change unless the inhibitor can be removed | ||
The enzyme adjusts its shape so that the substrate, but NOT the competitive inhibitor, can bind | ||
The substrate will bind to the competitive inhibitor and block its ability to bind to the enzyme |
1.2 points
QUESTION 12
What determines where in the genome a transcription regulator will bind?
Transcription regulators bind to the 5' UTR region of a gene | ||
Regulators bind via complementary base-pairing to certain DNA molecules | ||
Covalent bonds form between the transcription regulator and the atoms of the DNA backbone | ||
Every eukaryotic gene has a different transcription regulator that will bind to the 5' end of the gene | ||
Transcription regulators bind to specific DNA sequences via multiple weak non-covalent interactions |
1.2 points
QUESTION 13
What is the basic premise of cell theory?
DNA -> RNA -> protein | ||
All cells arise from pre-existing cells | ||
DNA provides the complete instructions to create a cell | ||
The identity of a cell is determined through gene expression patterns | ||
All cells contain the same four basic macromolecules |
1.2 points
QUESTION 14
What is the benefit of using BOTH the lac activator and the lac repressor to control gene expression?
Using both an activator and repressor enables cells to more accurately determine the amount of lactose available in the environment | ||
Enzymes to digest lactose are only made when energy is low and lactose is available | ||
The activator can override the inhibition of the lac operon by the repressor | ||
The repressor can control the enhancer, while the activator can control the promoter | ||
When neither the lac activator or repressor is present, expression of the lac operon is too high |
1.2 points
QUESTION 15
What is the histone code used for?
Phosphorylation and acetylation of DNA affect its ability to be compacted | ||
Changes to the sequence of DNA change whether DNA will wrap around histone proteins | ||
Covalent modifications of histones affect the ability of the transcription initiation complex to form | ||
Histones provide the codon sequences needed for translation to occur | ||
The histone code affects which amino acids will get added to a polypeptide |