Toothpick Biochemistry: Toothpickase
Name ______
Introduction:
Enzymes are proteins that are used as catalysts in biochemical reactions. A catalyst is something that controls the rate of a reaction without itself being used up. Often, enzymes are used to speed up the rate of a reaction. Any chemical reaction that is exergonic (i.e. gives off energy while it’s happening) will eventually happen spontaneously. However, the time frame for “spontaneously” is “sometime before the end of the universe.” Living organisms can’t wait that long, so they use enzymes to help these reactions happen faster.
Remember, enzymes are proteins – they will need to fold into their correct shape before they can serve their function. When an enzyme has folded correctly, the active site is ready to go. The active site is a small area on the surface of the enzyme where the substrate(s) temporarily bind to the enzyme. After the reaction has taken place, the new products that were formed disengage from the enzyme and float away, leaving the enzyme in perfect shape to do it all over again.
The average enzyme can repeat its reaction-helping magic about 1000 times per second. When an enzyme is working as fast as it can, that speed is known as Vmax. (V stands for “velocity,” and Vmax is usually expressed as a rate -- # molecules/second.) However, an enzyme doesn’t always work at its maximum speed. Vmax depends on several factors, including amount of substrate, competitive inhibitors of the enzyme, and temperature. This lab will explore these factors.
Congratulations – you’re an enzyme! In fact, you are toothpickase, a molecule that can break down toothpicks into two pieces. Pick up a toothpick, and snap it in half.
1. What is the reactant(s) in this situation?
2. What is the product(s)?
3. How would you describe your active site?
Take your pile of toothpicks, and create 4 piles of roughly 50 toothpicks each. Designate one person as toothpickase, and the other as data recorder. Place one pile in front of the enzyme. As the enzyme picks up toothpicks and snaps them in half, he/she should keep count of how many toothpicks he/she has metabolized. The data recorder will keep track of time and double-check the number of toothpicks metabolized.
*Metabolized toothpicks go back in the pile!* In the cell, the products of a reaction are still floating around in the enzyme’s general vicinity.
*Toothpickase must keep his/her eyes closed! Enzymes do not have eyes, and they do not know what they have picked up until they try to fit it into their active site.
*You can not break an already broken toothpick!* Enzymes are usually quite specialized, and toothpickase’s active site only recognizes whole toothpicks. (Another enzyme, toothpickpiecease, is needed to break down the toothpick pieces, and toothpickgluease is the only enzyme that can put the pieces back together again.)
4. How many toothpicks can toothpickase break in 30 seconds?
CONSIDER CHANGING TO “HOW LONG DOES IT TAKE TO BREAK 10 TOOTHPICKS?”
There may be times when toothpickase is not needed. For example, if the cell needs toothpicks to build its cytoskeleton, the last thing it wants is toothpickase breaking down all the toothpicks. So it needs a way to turn toothpickase off, or at least slow it down.
Add a handful of paperclips to a new pile of toothpicks, and mix them up well.
5. How many toothpicks is toothpickase able to break in 30 seconds?
6. Don’t actually try this, but how effective do you think toothpickase would be at metabolizing toothpicks if someone were tickling the enzyme?
7. How effective would toothpickase be if the enzyme had to plunge his/her hands into ice water for several minutes?
The previous three questions are different ways to inhibit an enzyme. You can plug up its active site, you can cause the active site to change its shape by poking the enzyme elsewhere on its ”body,” or you can remove heat energy by lowering the temperature.
Because enzymes are proteins, there are genes in the DNA that hold the instructions for making each enzyme. These genes, like any other genes, can be mutated. This would create a different nucleotide sequence, which may call for a different amino acid chain.
Mutate the toothpickase’s active site by having the enzyme cross his/her fingers on both hands.
8. How many toothpicks can be metabolized in 30 seconds?
Mutate a place away from the active site on the enzyme by having toothpickase stand on one foot (and uncross his/her fingers.)
9. Now how many toothpicks can the enzyme break down in 30 seconds?
10. Are all mutations harmful to an enzyme? Explain your answer.
Application Questions
11. One thing some real enzymes need that “toothpickase” does not is an energy source. What molecule serves as an energy source for enzymes? What could we use to simulate this in our toothpickase model? (http://www.indiana.edu/~oso/animations/seesaw.html can give you a hint.)
12. Certain bacteria called extremophiles prefer to live in boiling hot water – 212 degrees Farenheit. What problem with your proteins prevents you (a human) from living in such high temperatures (or, stated another way, what problem have these bacteria solved?)
13. Tay-Sachs disease is a illness that causes progressive destruction of the central nervous system. Tay-Sachs patients are missing the enzyme hexosaminidase-A, which breaks down a harmful lipid created as a waste product in nerve cells. The lipid builds up inside the nerve cells and eventually kills the cells, leading to brain damage and death. A family has just learned that their baby has Tay-Sachs disease. The father is very upset, saying that the disease must have run in his family. The nosy next-door neighbor says, “It can’t be your fault – everyone knows that you don’t pass your enzymes on to your children.” Who is correct?
14. Visit http://www.indiana.edu/~oso/animations/amylase.html and watch the animation. Be sure to watch both the close-up view and the less detailed view of the reaction.
a. In the less-detailed view, would you say that the enzyme is deliberately seeking out its substrate, or is it randomly bumping into it?
b. Based on your answer above, explain why colder temperatures slow down the speed at which enzymes work, and why warmer temperatures speed them up. (Can’t let it get too warm, of course. . . .) (http://www.indiana.edu/~oso/animations/liq_vs_gas.html will give you a hint if you’re stuck.)
15. Visit http://www.indiana.edu/~oso/animations/SN2%2BE.html and play with the animation.
a. In order for one of your muscles to contract, a nerve cell must deliver the molecule acetylcholine (ACh) to receptors on the muscle’s surface. As long as ACh is in the receptor, the muscle will stay contracted and will not relax. An enzyme, called acetylcholinesterase, removes the ACh from the receptors and breaks it down. Based on the information in the animation you watched, why do you need an acetylcholinesterase enzyme? Why can’t you just wait for the ACh to break down on its own?