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Chemical Investigations
Part I: Help from MOM: A Colorful Antacid Lab
Introduction:
Organisms are often very sensitive to the effect of acids and bases in their environment. They need to maintain a stable internal pH in order to survive—even in the event of environmental changes. Many naturally occurring biological, geological, and human-made chemicals are capable of stabilizing the environment’s pH in a process called buffering. This may allow organisms to better survive in diverse environments found throughout the earth.
A buffer is a mixture of a weak acid and its conjugate base, or a weak base and its conjugate acid. A buffer’s function is to absorb acids (H+ or H3O+ ions) or bases (OH– ions) so that pH changes very, very little. The bicarbonate-carbon dioxide buffer system, for example, keeps the pH of blood in humans between 7.3 and 7.5.
Milk of magnesia (MOM) and other antacids are bases that relieve heartburn by neutralizing the acid found in the stomach’s gastric juices. When hydrochloric acid and universal indicator are added to milk of magnesia, a dramatic rainbow of color changes is observed as the antacid neutralizes the simulated stomach acid.
Materials
Milk of magnesia (MOM), 20 mL Graduated cylinder, 25-mL or 50-mL
Hydrochloric acid, HCl, 3 M, approximately 20 mL Ice, crushed (or ice cubes)
Universal indicator solution, 4–5 mL Magnetic stirrer and stir bar
Water, distilled or deionized, 800 mL Pipets, thin-stem, disposable, 2
Beaker, 1-L (or other large beaker) Universal Indicator Color Chart
Safety Precautions
• Milk of magnesia that has been brought into the lab is considered a laboratory chemical and is intended for laboratory use only.
• Hydrochloric acid solution is toxic by ingestion, inhalation and is corrosive to skin and eyes.
• Universal indicator solution contains ethyl alcohol and is a flammable liquid.
• Wear chemical splash goggles, chemical-resistant gloves, and a chemical-resistant apron.
• Wash hands thoroughly with soap and water before leaving the laboratory.
• Follow all normal laboratory guidelines.
Please review current Material Safety Data Sheets for additional safety, handling, and disposal information.
Procedure
1. Measure 20 mL of milk of magnesia (MOM) using a graduated cylinder and pour it into a 1-L beaker.
2. Add a stir bar to the MOM solution and place the 1-L beaker on a magnetic stirrer. (If a magnetic stirrer is not available, use a stirring rod to mix the solution as other reactants are added in steps 3–5.)
3. Add water and crushed ice (or ice cubes) to give a total volume of approximately 800 mL. Turn on the stir plate so as to create a vortex in the mixture.
4. Add about 4–5 mL (about 2 pipets-full) of universal indicator solution. Watch as the white suspension of milk of magnesia turns to a deep purple color. The color indicates that the solution is basic.
5. Add 2–3 mL (1 pipet-full) of 3 M HCl. The mixture quickly turns red and then goes through the entire range of universal indicator color changes back to purple.
6. Repeat this process, adding HCl one pipet-full at a time, waiting after each addition until the mixture turns back to blue–purple.
7. The process can be repeated a number of times before all of the milk of magnesia has dissolved and reacted with the HCl. As more acid is added, the color changes will occur more rapidly and eventually the suspended solid in MOM will be completely dissolved. The final solution, when all the MOM has reacted, will be red and clear.
Disposal
Please consult your current Flinn Scientific Catalog/Reference Manual for proper disposal procedures. Neutralize the final solution with sodium carbonate or excess milk of magnesia according to Flinn suggested Disposal Method #24b. Excess milk of magnesia can be disposed of according to Flinn Suggested Disposal Method #26a solid waste disposal in landfill.
Discussion
Hydrochloric acid secreted in the stomach gives the gastric juice a pH of between 1.5 and 3.5, depending upon the amount of food within the stomach. The pH of an empty stomach is usually less than 2. When gastric juices contact the esophagus, the acid may irritate and partially digest the esophageal lining. The resulting heartburn is often treated with antacids. Antacid literally means “against acid.” Antacids are weak bases that work by neutralizing the acidic environment of the stomach. This demonstration uses the antacid milk of magnesia (MOM). The active ingredient in milk of magnesia is magnesium hydroxide, Mg(OH)2.
MOM works well for the demonstration because the magnesium hydroxide forms a suspension in water due to its very low solubility—0.0009 g/100 mL in cold water and 0.004 g/100 mL in hot water. This
limited solubility makes it an ideal compound for use in commercial antacids because, rather than dissolving all at once, it slowly dissolves as it reacts with and neutralizes stomach acid. As the “excess stomach acid” neutralizes the dissolved magnesium hydroxide, more magnesium hydroxide enters the solution from the solid suspension state until the solution is neutralized or all of the reactants are used up.
Universal indicator is added to the MOM suspension to help visualize the neutralization reaction as it occurs. The initial color of universal indicator in the MOM suspension is violet, corresponding to a basic solution (pH ≥ 10). (See the Universal Indicator Color Chart. When hydrochloric acid (the simulated “stomach acid”) is added, the mixture quickly turns red (pH 4) as the acid disperses throughout the beaker and neutralizes a small amount of dissolved magnesium hydroxide.
Some unreacted acid is still present, however, so the solution remains red. However, the unreacted acid causes more magnesium hydroxide from the suspension to gradually dissolve and react. As more of the magnesium hydroxide goes into solution, the excess acid is neutralized and eventually the solution turns blue or violet (pH 9–10) again, indicating excess magnesium hydroxide is present. The added universal indicator allows this process to be observed. During the process, the color of the mixture – 3 –cycles through the entire universal indicator color range—from red to orange to yellow to green to blue and finally back to violet.
By adding more “stomach acid,” the process can be repeated several times before all of the magnesium hydroxide dissolves and is neutralized. The final solution, after all the MOM has dissolved and reacted with HCl, is red and clear.
Universal Indicator Color Chart
|COLOR |
| |pH after number of drops added | |
|Material |Added |0 |
|1. | | |
|2. | | |
|3. | | |
|4. | | |
|5. | | |
|Average | | |
Part D: Capillary Action
Water has the ability to stick onto things (adhesion) and stick to itself (cohesion). These two properties together allow water to defy gravity and climb up tubes of small diameter. This is called capillary action.
1. Obtain a stalk of celery that has been soaking in water.
2. Holding the celery stalk under water, use a razor blade to make a new horizontal cut on the far end of the celery (away from the leaves).
3. Measure 100 mL of water into a 250 mL beaker and add 10 drops of food coloring. Place the cut end of the celery into the colored water.
4. After 50 minutes remove the celery from the colored water and dry it off with a paper towel.
5. Observe the cut end of the celery.
6. Using a scaple and a ruler slice off 2 mm from the end of the celery.
7. Observe the cut end of the celery. Does it appear the same? Keep cutting in 2 mm increments until there is a change in appearance.
a. Determine the rate at which the color water moved in the celery.
b. Did the colored water travel through all parts of the celery? Explain.
c. If the water traveled differently in different places, suggest a reason for the difference you observed.
Part E: Specific Heat of Water
For such a small molecule, water has a very high specific heat. This means it takes a lot of energy to raise the temperature of water. Another important property is the range of temperature for which water remains a liquid. When water evaporates, like from sweat, it also removes a lot of heat from our body. In this activity, we'll conduct a simple experiment to observe the specific heat capacity of water. By doing so, we'll be able to gain some insight about the lag time of the climate system's response to external forcing.
Review: The specific heat is the amount of heat per unit mass required to raise the temperature by one degree Celsius. The relationship between heat and temperature change is usually expressed in the form shown below where c is the specific heat. The relationship does not apply if a phase change is encountered, because the heat added or removed during a phase change does not change the temperature.
(If time allows, we can use the Vernier temperature probe and LabQuest for this portion of the lab.)
1. Turn a hot plate on to a temperature of your choice. Note the setting in your lab book.
2. Take the mass of a 250mL beaker.
3. Place 100 mL of room temperature water in the beaker.
4. Determine the mass of the water.
5. Measure the starting temperature of the water.
6. Carefully place the beaker of water on the preheated hot plate.
7. Measure the temperature of the water every 30 seconds.
8. When the water boils, note the time.
9. Remove the beaker from the hot plate and place it on some type of insulated maerial (such as a hot pad. Be careful removing the beaker!
10. Continue to make regular measurements of the temperature of the water until it cools back down to the initial temperature from step 3.
11. Calculate the specific heat of water using your data.
12. Repeat this procedure using salt water with the same concentration of salt found in ocean water, approximately 3.5%.
LAB NOTEBOOK: Develop an Inquiry Plan to test, measure or manipulate a property of water.
• Researchable Question
• Hypothesis
o Variables: Independent (Manipulated) variable Dependent (Responding) variable, and Controlled variable(s)
• Materials List
• Procedure
• Safety Concerns
• Collecting and Presenting Data
o Data Table (if applicable)
• Analyzing and Interpreting Results*
• Conclusion*
*Complete these portions if the experiment is actually done.
Organic Chemistry
Introduction:
We frequently hear the term "organic" in everyday language where it describes or refers to substances that are "natural". This is probably a result of the notion of early scientists that all organic compounds came from living systems and possessed a "vital force". However, chemists learned over 170 years ago that this is not the case. Organic compounds are major components of living systems, but chemists can make many of them in the laboratory from substances that have no direct connection with living systems. Chemically speaking, a pure sample of an organic compound such as Vitamin C prepared in a laboratory is chemically identical to a pure sample of Vitamin C isolated from a natural source such as an orange or
other citrus fruit.
The number of different types of atoms in organic compounds suggests they are structurally complex. Fortunately, we find these atoms in a relatively few specific arrangements because of their preferred bonding characteristics. For example, C atoms primarily bond to each other to form the molecular skeleton or backbone of organic molecules, while H atoms bond to the various C atoms, or to other atoms such as N and O, almost like a "skin" surrounding the molecule. You can see some of these features in the organic molecule lauric acid that is one of a group of molecules called fatty acids. [graphic 1.1] Since atoms such as N, O, and the halogens (generally referred to as X) connect to the carbon skeleton in characteristic ways that determine the properties of a molecule, we call these groups of atoms functional groups. Functional groups define the class to which the organic molecule belongs.
Part IV: Working with Molecular Models
Pattern matching is an important skill. Biologists are constantly looking for significant patterns in nature. Even biological molecules are pattern matchers. Biological enzymes are a good example - each enzyme typically recognizes one and only one type of molecule or pair of molecules.
Carbohydrates (See pg. 71-73 of your textbook.)
8. Build two glucose molecules. Draw a stick figure of one of your glucose molecules in the appropriate place within the questions. Number your carbons (appropriately!) and label the hydroxyl groups on carbons 1 and 4.
9. “Bond” the two glucose molecules together to make the disaccharide maltose. What was removed in the process? What kind of bond was formed?
Proteins (See pg. 79 of your textbook.)
10. Build two different amino acids. Draw a stick figure of your amino acids in the appropriate place within the questions. Name the amino acids and label the amine and carboxyl groups for each.
11. “Bond” the two amino acids together to make a dipeptide. What was removed in the process? What kind of bond was formed?
Lipids (See pg. 75 of your textbook.)
12. Build a fatty acid chain (make a short one!) and a glycerol. Draw a stick figure of your molecules in the appropriate place within the questions. Name the hydroxyl groups and carboxyl group for each.
13. “Bond” the glycerol and fatty acid chain together to make a “tri”-glyceride. (You only need to make one fatty acid chain although three would be needed to make a triglyceride. What kind of bond was formed?
Nucleic Acids (See pg. 87 of your textbook.)
14. Build two nucleotide molecules, one a purine and one a pyrimidine, making sure they are compatible. Draw a stick figure of one of the nucleotides in the appropriate place with the questions. Name the phosphate group, sugar, and nitrogenous base for the molecule.
15. You will “bond” the two nucleotides together in two different ways. First bond them together as if they were forming one side of the ladder. Second bond them together as if they were forming one rung of the ladder. What kind of bond was formed to make the side of the ladder? What kind of bond was formed to make the rung of the ladder?
Part V: Amino Acid Starter Kit Building Blocks of Proteins
Introduction
Proteins are more than an important part of your diet. Proteins are complex molecular machines that are involved in nearly all of your cellular functions. Each protein has a specific shape (structure) that enables it to carry out its specific job (function).
A core idea in the life sciences is that there is a fundamental relationship between a biological structure and the function it must perform. At the macro level, Darwin recognized that the structure of a finch’s beak was related to the food it ate. This fundamental structure-function relationship is also true at all levels below the macro level, including proteins and other structures at the molecular level.
In this activity, you will explore the structure of proteins and the chemical interactions that drive each protein to fold into its specific structure, as noted below.
• Each protein is made of a specific sequence of amino acids. There are 20 amino acids found in proteins.
• Each amino acid consists of two parts — a backbone and a sidechain. The backbone is the same in all 20 amino acids and the sidechain is different in each one.
• Each sidechain consists of a unique combination of atoms which determines its 3D shape and its chemical properties.
• Based on the atoms in each amino acid sidechain, it could be hydrophobic, hydrophilic, acidic (negatively charged), or basic (positively charged).
• When different amino acids join together to make a protein, the unique properties of each amino acid determine how the protein folds into its final 3D shape. The shape of the protein makes it possible to perform a specific function in our cells.
Preparation
The activities described in this handout primarily focus on amino acid sidechains. They will help you understand how the unique properties of each sidechain contribute to the structure and function of a protein.
First look at the components in your Amino Acid Starter Kit. Make sure your 1-group set has:
1. 1 Chemical Properties Circle
2. 1 Laminated Amino Acid Sidechain List
3. 4’ Mini-Toober
4. 1 Set of Red and Blue Endcaps
5. 22 Clear Bumpers
6. 22 Amino Acid Sidechains
-1 each of the 20 Amino Acids
-1 additional cysteine and
-1 additional histidine
7. 22 Plastic Clips
-8 yellow
-8 white
-2 blue
-2 red
-2 green
8. 6 Hydrogen Bond Connectors
9. Chemical Properties Circle & Amino Acid Chart
Hydrophobic and Hydrophilic Properties
• Hydrophobic sidechains are also referred to as non-polar sidechains.
• Hydrophilic sidechains are also referred to as polar sidechains.
Acidic (Negatively Charged) and Basic (Positively Charged) Properties
Lemon and fruit juices, vinegar and phosphoric acid (in dark sodas) are common household acids. Acids taste sour and are typically liquids.
Tums®, baking soda, drain cleaner, and soap are common bases. Bases taste bitter and can be a liquid or solid.
What happens when you mix lemon juice or vinegar with baking soda? They neutralize each other, in a bubbling chemical reaction. (If available, give it a try!)
The colored areas on the Chemical Properties Circle, the color coding on the Amino Acid Sidechain List, the key below and the colored clips show the chemical properties of sidechains.
KEY
Hydrophobic Sidechains are Yellow
Hydrophilic Sidechains are White
Acidic Sidechains are Red
Basic Sidechains are Blue
Cysteine Sidechains are Green
Amino Acid Sidechain List.
Directions
Select any sidechain and a colored clip that corresponds to the property of the sidechain. Insert the sidechain into the clip.
Place each amino acid sidechain attached to its clip on the bumper near its name and abbreviations. You will need to consult the Amino Acid Sidechain List in your kit to find the name of each sidechain, so you can position it correctly on the circle.
Insert sidechain into clip.
Place clip (with sidechain attached) onto the bumper.
After each sidechain has been correctly positioned on the circle, look at the colored sheres in each sidechain. Scientists established a CPK coloring scheme (see chart below) to make it easier to identify specific atoms in models of molecular structures.
KEY
Carbon is Gray
Oxygen is Red
Nitrogen is Blue
Hydrogen is White
Sulfur is Yellow
Folding a 15-Amino Acid Protein
Once you have explored the chemical properties and atomic composition of each sidechain, think about how proteins spontaneously fold into their 3D shapes.
Predict what causes proteins to fold into their 3D shapes.
1. Unwind the 4-foot mini-toober (foam-covered wire) that is in your kit. Place a blue end cap on one end and the red end cap on the other end. The blue end cap represents the N-terminus (the beginning) of the protein and the red end cap represents the C-terminus (the end) of the protein.
2. Choose 15 sidechains from the chemical properties circle as indicated in the chart below.
Mix the Sidechains together and place them (in any order you choose) on your mini-toober.
KEY
6 Hydrophobic sidechains
2 Acidic sidechains
2 Basic sidechains
2 Cysteine sidechains
3 Hydrophilic sidechains
3. You may want to use a ruler to place your sidechains on you mini-toober.
Beginning at the N-terminus of your mini-toober, measure about three inches from the end of your mini-toober and slide the first colored clip with its sidechain onto the mini-toober. Place the rest of the clips three inches apart on your mini-toober until all are attached to the mini-toober.
4. Now you can begin to fold your 15-amino acid protein according to the chemical properties of its sidechains. Remember all of these chemical properties affect the protein at the same time.
Hydrophobic Sidechains
Start by folding your protein so that all of the hydrophobic (non-polar) sidechains are buried on the inside of your protein, where they will be hidden from polar water molecules.
Acidic & Basic Sidechains
Fold your protein so the acidic and basic (charged) sidechains are on the outside surface of the protein. Place one negative (acidic) sidechain with one positive (basic) sidechain so that they come within one inch of each other and neutralize each other. This positive-negative pairing helps stabilize your protein.
Note: As you continue to fold your protein and apply each new property listed below, you will probably find that some of the sidechains you previously positioned are no longer in place. For example, when you paired a negatively charged sidechain with a positively charged one, some of the hydrophobic sidechains probably moved to the outer surface of your protein. Continue to fold until the hydrophobic ones are buried on the inside again. Find a shape in which all the properties apply simultaneously.
Cysteine Sidechains
Fold your protein so that the two cysteine sidechains are positioned opposite each other on the inside of the protein where they can form a covalent-disulfide bond that helps stabilize your protein.
Hydrophilic Sidechains
Continue to fold you protein making sure that your hydrophilic (polar) sidechains are also on the outside surface of your protein where they can hydrogen bond with water.
The final shape of your protein when it is folded is called the tertiary structure.
Part VI: Enzyme Action: Testing Catalase Activity - (Method 1–O2 Gas Sensor)
Introduction:
Many organisms can decompose hydrogen peroxide (H2O2) enzymatically. Enzymes are globular proteins, responsible for most of the chemical activities of living organisms. They act as catalysts, substances that speed up chemical reactions without being destroyed or altered during the process. Enzymes are extremely efficient and may be used over and over again. One enzyme may catalyze thousands of reactions every second. Both the temperature and the pH at which enzymes function are extremely important. Most organisms have a preferred temperature range in which they survive, and their enzymes most likely function best within that temperature range. If the environment of the enzyme is too acidic, or too basic, the enzyme may irreversibly denature, or unravel, until it no longer has the shape necessary for proper functioning.
H2O2 is toxic to most living organisms. Many organisms are capable of enzymatically destroying the H2O2 before it can do much damage. H2O2 can be converted to oxygen and water, as follows:
2 H2O2 [pic] 2 H2O + O2
Although this reaction occurs spontaneously, enzymes increase the rate considerably. At least two different enzymes are known to catalyze this reaction: catalase, found in animals and protists, and peroxidase, found in plants. A great deal can be learned about enzymes by studying the rates of enzyme-catalyzed reactions. The rate of a chemical reaction may be studied in a number of ways including:
measuring the rate of appearance of a product (in this case, O2, which is given off as a gas)
measuring the rate of disappearance of substrate (in this case, H2O2)
measuring the pressure of the product as it appears (in this case, O2).
In this experiment, you will measure the rate of enzyme activity under various conditions, such as different enzyme concentrations, pH values, and temperatures. It is possible to measure the concentration of oxygen gas formed as H2O2 is destroyed using an O2 Gas Sensor.
At the start of the reaction, there is no product, and the concentration is the same as the atmosphere. After a short time, oxygen accumulates at a rather constant rate. The slope of the curve at this initial time is constant and is called the initial rate. As the peroxide is destroyed, less of it is available to react and the O2 is produced at lower rates. When no more peroxide is left, O2 is no longer produced.
Objectives
In this experiment, you will
Use an O2 Gas Sensor to measure the production of oxygen gas as hydrogen peroxide is destroyed by the enzyme catalase or peroxidase at various enzyme concentrations.
Measure and compare the initial rates of reaction for this enzyme when different concentrations of enzyme react with H2O2.
Measure the production of oxygen gas as hydrogen peroxide is destroyed by the enzyme catalase or peroxidase at various temperatures.
Measure and compare the initial rates of reaction for the enzyme at each temperature.
Measure the production of oxygen gas as hydrogen peroxide is destroyed by the enzyme catalase or peroxidase at various pH values.
Measure and compare the initial rates of reaction for the enzyme at each pH value.
MATERIALS
|LabQuest |enzyme suspension |250 mL Nalgene bottle |
|LabQuest App |ice |3.0% H2O2 |
|Vernier O2 Gas Sensor |pH buffers |Logger Pro |
|400 mL beaker |test tube rack | |
|10 mL graduated cylinder |thermometer | |
|three 18 ( 150 mm test tubes |three dropper pipettes | |
PROCEDURE
1. Obtain and wear goggles.
2. Connect the O2 Gas Sensor to LabQuest and choose New from the File menu. If you have an older sensor that does not auto-ID, manually set up the sensor.
3. On the Meter screen, tap Rate. Change the data-collection rate to 0.2 samples/second and the data-collection length to 180 seconds.
Part A: Testing the Effect of Enzyme Concentration
4. Place three test tubes in a rack and label them 1, 2, and 3. Fill each test tube with 5 mL of 3.0% H2O2 and 5 mL of water.
5. Initiate the enzyme catalyzed reaction.
a. Using a clean dropper pipette, add 5 drops of enzyme suspension to test tube 1.
b. Begin timing with a stopwatch or clock.
c. Cover the opening of the test tube with a finger and gently invert the test tube two times.
d. Pour the contents of the test tube into a clean 250 mL Nalgene bottle.
e. Place the O2 Gas Sensor into the bottle as shown in Figure 1. Gently push the sensor down into the bottle until it stops. The sensor is designed to seal the bottle with minimal force.
f. When 30 seconds has passed, start data collection.
6. When data collection is complete, a graph of O2 gas vs. time will be displayed. Remove the O2 Gas Sensor from the Nalgene bottle. Rinse the bottle with water and dry with a paper towel.
7. Perform a linear regression to calculate the rate of reaction.
a. Choose Curve Fit from the Analyze menu.
b. Select Linear for the Fit Equation. The linear-regression statistics for these two data columns are displayed for the equation in the form:
y = mx + b
c. Enter the absolute value of the slope, m, as the reaction rate in Table 2.
d. Select OK.
8. Store the data from the first run by tapping the File Cabinet icon.
9. Find the rate of enzyme activity for test tubes 2, and 3:
a. Add 10 drops of the enzyme solution to test tube 2. Repeat Steps 5–8.
b. Add 20 drops of the enzyme solution to test tube 3. Repeat Steps 5–7.
10. Graph all three runs of data on a single graph.
a. Tap Run 3, and select All Runs. All three runs will now be displayed on the same graph axes.
b. Use the displayed graph and the data in Table 2 to answer the questions for Part A.
Part B: Testing the Effect of Temperature
Your teacher will assign a temperature range for your lab group to test. Depending on your assigned temperature range, set up your water bath as described below. Place a thermometer in your water bath to assist in maintaining the proper temperature.
0–5°C: 400 mL beaker filled with ice and water.
20–25°C: No water bath needed to maintain room temperature.
30–35°C: 400 mL beaker filled very warm water.
50–55°C: 400 mL beaker filled hot water.
11. Rinse the three numbered test tubes used for Part A. Fill each test tube with 5 mL of 3.0% H2O2 and 5 mL of water then place the test tubes in the water bath. The test tubes should be in the water bath for 5 minutes before proceeding to Step 15. Record the temperature of the water bath, as indicated on the thermometer, in the space provided in Table 3.
12. Tap Table. Choose Clear All Data from the Table menu.
13. Tap Graph to display the graph.
14. Find the rate of enzyme activity for test tubes 1, 2, and 3:
a. Add 10 drops of the enzyme solution to test tube 1. Repeat Steps 5–7. Record the reaction rate in Table 3.
b. Add 10 drops of the enzyme solution to test tube 2. Repeat Steps 5–7. Record the reaction rate in Table 3.
c. Add 10 drops of the enzyme solution to test tube 3. Repeat Steps 5–7. Record the reaction rate in Table 3.
15. Calculate the average rate for the three trials you tested. Record the average in Table 3.
16. Record the average rate and the temperature of your water bath from Table 3 on the class chalkboard. When the entire class has reported their data on the chalkboard, record the class data in Table 4.
Part C: Testing the Effect of pH
17. Place three clean test tubes in a rack and label them pH 4, pH 7, and pH 10.
18. Add 5 mL of 3% H2O2 and 5 mL of a pH buffer to each test tube, as in Table 1.
|Table 1 |
|pH of buffer |Volume of 3% H2O2 |Volume of buffer |
| |(mL) |(mL) |
|pH 4 |5 |5 |
|pH 7 |5 |5 |
|pH 10 |5 |5 |
19. Tap Table. Choose Clear All Data from the Table menu.
20. Tap Graph to display the graph.
21. Using the test tube labeled pH 4, add 10 drops of enzyme solution and repeat Steps 5–8.
22. Using the test tube labeled pH 7, add 10 drops of enzyme solution and repeat Steps 5–8.
23. Using the test tube labeled pH 10, add 10 drops of enzyme solution and repeat Steps 5–7.
24. Graph all three runs of data on a single graph
a. Tap Run 3 and select All Runs. All three runs will now be displayed on the same graph axes.
b. Use the displayed graph and the data in Table 5 to answer the questions for Part C.
LAB NOTEBOOK: Develop an Inquiry Plan to test one of the following:
Select one of the following questions and design and experiment to test your hypothesis:
a. Different organisms often live in very different habitats. Design a series of experiments to investigate how different types of organisms might affect the rate of enzyme activity. Consider testing a plant, an animal, and a protist.
b. Presumably, at higher concentrations of H2O2, there is a greater chance that an enzyme molecule might collide with H2O2. If so, the concentration of H2O2 might alter the rate of oxygen production. Design a series of experiments to investigate how differing concentrations of the substrate hydrogen peroxide might affect the rate of enzyme activity.
c. Design an experiment to determine the effect of boiling the catalase on the rate of reaction.
d. Explain how environmental factors affect the rate of enzyme-catalyzed reactions.
• Researchable Question
• Hypothesis
o Variables: Independent (Manipulated) variable Dependent (Responding) variable, and Controlled variable(s)
• Materials List
• Procedure
• Safety Concerns
• Collecting and Presenting Data
o Data Table (if applicable)
• Analyzing and Interpreting Results*
• Conclusion*
*Complete these portions if the experiment is actually done.
Part VII: Pineapple Enzymes & JELLO Molds
Adapted by Kim B. Foglia • • 2005-2006
Background:
If you have ever made Jell-O by cooking the powder that comes in a box, you may have noticed the warning on the instructions that tell you not to add fresh or frozen pineapple to the gelatin. Have you ever wondered why? Well, most of cooking is really Kitchen Chemistry and this is an example. In this lab, you will be designing an experiment to test what is really happening when you add pineapple to gelatin. You know enough organic chemistry now to figure this out.
First, you need a little background about gelatin… and it may be more than you ever wanted to know. Do you know what Jell-O is really made out of? Are you ready? That sweet colorful treat is actually made out of hides, bones, and inedible connecting tissue from animals butchered for meat. No? Yup!
All gelatin (including those made for photographic and laboratory use, as well as for desserts) is made out of discarded animal parts — the tough parts: bone and skin. And all these tough parts are made of proteins. In fact, the extracted gelatin is a protein. So, why do you think gelatin gets thick and jelly-like when you cook it? (We’ll come back to that later.)
Gelatin can be extracted from any kind of animal, but cows are most common. If your Mom or Dad have ever made a batch of chicken soup from scratch, you've probably seen how it gets stiff and Jell-O like after it sits in the fridge… that's because boiling the chicken in water extracts the gelatin from the carcass (bones & cartilage), just like a miniature version of the commercial gelatin factories! Commercial gelatin making starts by grinding up bones. The crushed bones are then soaked in a strong base (high pH) to soften them, and then passed through progressively stronger acid (low pH) solutions, until the end result isn't recognizable as bones at all! Then the whole mess is boiled for hours to extract the gelatin… and this part really makes a stink! Finally, the gelatin layer is skimmed off the boiling pot, and dried into a powder. With added sugar, flavorings, and artificial color, it's ready to become a jiggly dessert!
And now that you know what Jell-O's made from, why don't you put some on the table tonight? Your guests will be delighted when you share your new knowledge with them in the middle of a luscious spoonful of dessert! By the way, this whole process of extracting gelatin from bone was originally developed in 1845 by an engineer, Peter Cooper — the man who Cooper Union (in NYC) is named after. Sometime later (1895), Pearl B. Wait, a cough syrup manufacturer, bought the patent from Peter Cooper and adapted Cooper's gelatin dessert into an entirely prepackaged form, which his wife, May David Wait, named "Jell-O." The rest is history...
Made from bone… made from protein… so it must be tough stuff! So why can’t you put fresh pineapple in it? Let’s learn a bit about pineapple. The pineapple plant (Ananas comosus) is a monocot, or grass-like plant, that belongs to the bromeliad family. It is thought to have originated in Brazil. In the 1950s, pineapple became the United States’ second most important fruit and Hawaii led the world in both quantity and quality of pineapples. However, times have changed and now, all canned pineapple comes from overseas, largely from the Philippines.
As with some other tropical fruits, the pineapple fruit contains an enzyme that breaks down, or digests, protein. This protease (protein-digesting) enzyme in pineapple is called bromelain, which is extracted and sold in such products as Schilling's Meat Tenderizer. Papaya, another tropical fruit, also contains an enzyme, called papain, that digest protein. It can be found in Accent Meat Tenderizer.
Materials:
Fresh pineapple
Canned pineapple
Frozen pineapple
Jell-o
Beakers
Boiling & ice water
Test tubes & rack
Spoons, stirring rods
Knife for chopping pineapple
Procedure:
In this lab, you will be given an array of materials and you will be asked to design your own experiment to test the effect of pineapple on gelatin. The goal is to understand what is actually going on in the pineapple-gelatin mix at a chemical level as well as understanding what affects the function of enzymes.
Design a controlled experiment that shows the effect of raw pineapple on gelatin. Make sure your experiment description includes the following:
LAB NOTEBOOK: Develop an Inquiry Plan to test, measure or manipulate a property of water.
• Researchable Question
• Hypothesis
o Variables: Independent (Manipulated) variable Dependent (Responding) variable, and Controlled variable(s)
• Materials List
• Procedure
• Safety Concerns
• Collecting and Presenting Data
o Data Table (if applicable)
• Analyzing and Interpreting Results*
• Conclusion*
*Complete these portions if the experiment is actually done.
Questions
Part I: Help from mom
1. WHAT CAUSES HEARTBURN?
2. How is the lining of the stomach different from the lining of the esophagus?
3. How would this activity be affected if hot water were used instead of ice water?
4. Why is magnesium hydroxide an ideal compound for antibiotics?
5. Why do you need to shake MOM before taking?
6. MOM is also used for constipation. Although MOM can be used as an antacid in the stomach explain how it can be used as a laxative in the intestines.
Part II: investigating buffers with vernier
1. DETERMINE THE TOTAL PH CHANGE OF YOUR BAKING SODA SAMPLE.
a. Determine the change of pH (ΔpH) upon the addition of acid.
b. Determine the ΔpH upon the addition of base.
2. Subtract the ΔpH for the acid from the ΔpH for the base to determine the total pH change.
3. Is a baking soda solution acidic, or is it basic? How can you tell which it is?
4. What was the effect of adding HCl? Why did this happen?
5. What was the effect of adding NaOH? Why did this happen?
6. List five materials whose buffering action might be interesting.
7. List two biological buffer systems.
8. List at least one researchable question concerning a set of buffers or a buffer system.
PART III: PROPERTIES OF WATER
Part A: Polarity
1. Label the diagram of water from what you have learned in class. Make sure you label the oxygen, hydrogen (2), electrons, protons, and polar charges.
2. Dissolving NaCl:
a. How long did it take the NaCl to dissolve in the water?
b. Which is the solvent?
c. Which is the solute?
d. What is the resulting solution?
Part B: Hydrogen Bonding, Expansion on Freezing, Specific Heat, Evaporative Cooling
3. Label the 4 hydrogen bonds shown in the below diagram.
4. Label the following diagram and explain to the side why these hydrogen bonds are really attractions rather than bonds.
a. What causes polarity?
b. Why does polarity allow water to be such a good solvent?
5. Measure 10 grams of NaCl and add this to a beaker of 100 ml water.
6. Water expands when it freezes becoming less dense as a solid than it is as a liquid. Describe a test that you could complete at home to prove water expands as it freezes.
Part C: Adhesion, Cohesion, Surface Tension
Give the data table a title:
|Trial |Tap Water |Salt Water |
|1. | | |
|2. | | |
|3. | | |
|4. | | |
|5. | | |
|Average | | |
Part D: Capillary Action
7. Observe the cut end of the celery. Does it appear the same? Keep cutting in 2 mm increments until there is a change in appearance.
a. Determine the rate at which the color water moved in the celery.
b. Did the colored water travel through all parts of the celery? Explain.
c. If the water traveled differently in different places, suggest a reason for the difference you observed.
Part E: Specific Heat of Water
8. What is the accepted specific heat of fresh water?
9. What is your calculated specific heat for fresh water and “ocean” water?
10. Draw a graph and plot your two sets of data.
11. Design a data table showing the relevant data from this experiment. Ex. the rate of change (slope), time to boil, time to cool, etc.
12. How long did it take each pot of water to boil?
13. How long did it take each one to cool back down?
14. Eyeball a best fit function to the the water-heating-up data for each experiment. What do these functions look like (linear? curved? could you write an equation down to describe them?) What is indicated by the shapes of these functions? Were they affected by the changes you made between experiments?
15. Eyeball a best fit function to the the water-cooling-down data for each experiment. What do these functions look like? Are they all similar to each other? Do they have the same form as the water-heating-up functions? Discuss why or why not.
General Water Questions
16. How does electronegativity influence polarity?
17. Explain what a hydrogen bond is (as compared to covalent and ionic bonds).
18. Using the terms of hydrogen bond and cohesion, explain which type of water, regular or salt, has more cohesion.
19. Using the data below, create a graph to demonstrate the heating curve of water. The water starts out as ice and is heated until it is all water vapor. When you are finished with the graph, label the areas on the graph as: ice, water, steam, melting, or evaporating. Donʼt forget to give it a title and completely label the axes.
|Minutes |Degrees Celcius |Minutes |Degrees Celcius |
| | | | |
| | | | |
|Carbohydrate | | | |
| | | | |
| | | | |
| | | | |
| | | | |
|Protein | | | |
| | | | |
| | | | |
| | | | |
| | | | |
|Lipid | | | |
| | | | |
| | | | |
| | | | |
| | | | |
|Nucleic Acid | | | |
| | | | |
| | | | |
1. Kind of hard question??? Chemical equilibrium between the linear and ring structures greatly favors the formation of rings. Comparing the linear form of glucose and the ring form of glucose, you will see that the linear from of glucose has a carbonyl (C=O) group not found in the ring form. Why? How can they both have the formula C6H12O6? (See pg. 71 and study the diagrams at the top!)
PART V: AMINO ACID STARTER KIT
1. Hydrophobic sidechains primarily contain __________________ atoms.
2. Acidic sidechains contain two ____________________ atoms. This is called a carboxylic acid functional group.
3. Basic sidechains contain ____________________ atoms. This is called an amino functional group.
4. Hydrophilic sidechains have various combinations of _________________________________.
5. An exception to the above observation is:
Predict what causes proteins to fold into their 3D shapes.
6. Which sidechains might position themselves on the interior of a protein, where they are shielded from water?
7. From your experience with static electricity, which sidechains might be attracted to each other?
8. Would the final shape of a protein be a high energy state or a low energy state for all of the atoms in the structure?
9. Why?
10. This drawing represents the backbone section of an amino acid. What do you think the clips represent?
11. What happened as you continued to fold your protein and applied each new chemical property to your protein?
12. Were you able to fold your protein, so that all of the chemical properties were in effect at the same time?
13. If not, do you have any ideas why you weren’t able to fold your protein in a way that allowed all of the chemical properties to be in effect simultaneously?
14. Did your protein look like the proteins other students folded? Explain.
15. How many different proteins, 15 amino acid long, could you make given an unlimited number of each of the 20 amino acids?
16. Most real proteins are actually in the range of 300 amino acids long. How many different possible proteins, 300 amino acids in length, could exist?
17. Research how many different proteins are found in the human body. Hint: how many different genes are there in the human genome*?
18. Assuming that all human proteins are 300 amino acids long, what fraction of the total number of possible different proteins is found in the human body?
19. Why do you think there are fewer actual proteins than possible ones?
20. How could you use your model to show how genes can code for multiple proteins through the process of alternative splicing?
* Completed in 2003, the Human Genome Project (HGP) was a 13-year project coordinated by the U.S. Department of Energy and the National Institutes of Health. During the early years of the HGP, the Wellcome Trust (U.K.) became a major partner; additional contributions came from Japan, France, Germany, China, and others.
Project goals were to:
• Identify all of the approximately 20,000-25,000 genes in human DNA,
• Determine the sequences of the 3 billion chemical base pairs that make up human DNA,
• Store this information in databases,
• Improve tools for data analysis,
• Transfer related technologies to the private sector, and
• Address the ethical, legal, and social issues (ELSI) that may arise from the project.**
** U.S. Department of Energy Genome Programs website Genome/home.shtml
PART VI: ENZYME ACTION: TESTING CATALASE
Part A: Effect of Enzyme Concentration
|Table 2 |
|Test tube label |Slope, or rate (%/s) |
| 5 Drops | |
|10 Drops | |
|20 Drops | |
Part B: Effect of Temperature
|Table 3 | |Table 4 (Class data) |
|Test tube label |Slope, or rate (%/s) | |Temperature tested |Average rate |
|Trial 1 | | | | |
|Trial 2 | | | | |
|Trial 3 | | | | |
|Average | | | | |
|Temperature range:____(C | | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
| | | | | |
Part C: Effect of pH
|Table 5 |
|Test tube label |Slope, or rate (%/s) |
|pH 4 | |
|pH 7 | |
|pH 10 | |
PROCESSING THE DATA
For Part B of this experiment, make a graph of the rate of enzyme activity vs. temperature by hand or by using Logger Pro software. Plot the rate values for the class data in Table 4 on the y-axis and the temperature on the x-axis. Use this graph to answer the questions for Part B.
QUESTIONS
Part A: Effect of Enzyme Concentration
1. How does changing the concentration of enzyme affect the rate of decomposition of H2O2?
2. If one increases the concentration of enzyme to thirty drops, what do you think will happen to the rate of reaction? Predict what the rate would be for 30 drops.
Part B: Effect of Temperature
3. At what temperature is the rate of enzyme activity the highest? Lowest? Explain.
4. How does changing the temperature affect the rate of enzyme activity? Does this follow a pattern you anticipated?
5. Why might the enzyme activity decrease at very high temperatures?
Part C: Effect of pH
6. At what pH is the rate of enzyme activity the highest? Lowest?
7. How does changing the pH affect the rate of enzyme activity?
PART VII: PINEAPPLES AND JELLO MOLDS
1. Clearly describe the results of your experiment. In which test tubes did the gelatin jell, which did not.
2. Clearly explain the results of your experiment. Why did some test tubes of gelatin jell, why did others not. Be specific!
3. What is the enzyme in your experiment?
4. What is the substrate in your experiment?
5. What is (are) the product(s) in your experiment?
6. What type of organic molecule is gelatin?
7. What type of organic molecule is bromelain?
8. Write a “word equation” to describe the chemical reaction that occurs when pineapple is mixed with the gelatin.
9. Is the reaction of bromelain and gelatin dehydration synthesis or hydrolysis? Explain.
10. Why were the results of the freshly cooked pineapple different than the results of the fresh, raw pineapple? Be specific!
11. What is meat tenderizer and what does it do?
12. Design an experiment to test at what specific temperature the pineapple enzyme denatures.
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Figure 2
Figure 1.
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