Using Genetics To Treat Disease

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* This case study presents a fictitious scenario, but one that is based upon clinical observations.

† Background information on Acute Lymphocytic (Lymphoblastic) Leukemia modified from Satake, N., Acute Lymphoblastic Leukemia, http://www.emedicine.com/ped/topic2587.htm. Last accessed: 07/08/09.

“Pharmacogenetics” by Jeanne Ting Chowning Page 1

by

Jeanne Ting Chowning Department of Education, Northwest Association for Biomedical Research

Part I – Acute Lymphocytic (Lymphoblastic) Leukemia It’s called the children’s ward. For two teenagers who have been recently diagnosed with leukemia, it seems insulting to have their lives hijacked by doctors and nurses with stuffed animals clipped to their stethoscopes.

Laura is a forward on her school soccer team and leads the league in scoring. For the last four months, she has been really tired, but nothing seemed really wrong until her legs became covered with bruises. Just pressing her fingers on her skin was practically enough to make a bruise. It didn’t seem real when her doctor, Jane Ryder, diagnosed her with Acute Lymphocytic (or Lymphoblastic) Leukemia (ALL), or when she told her that ALL is the most common malignant (spreading) cancer found in children. She’s 14 years old; she’s not a child!

Beth is 13 and looks remarkably like Laura. Both have straight dark hair, large brown eyes, and tall slender builds. Beth has never been that athletic; she prefers reading and theater. She’s hoping to be part of the drama team next year when she goes to high school, even though she’ll only be a freshman. But she’s been missing a lot of school because of one virus after another, lots of fevers and night sweats, then that rash in the fall. Now she’s in a hospital, and it seems like the only people she sees are her parents, Dr. Ryder, and the nurses.

Laura and Beth both have ALL, which arises from the uncontrolled growth of immature lymphocytes (a type of white blood cell, or leukocyte). These cells, which are “stuck” in an early stage of development, become so numerous that they crowd out normal blood cells. Each year about 30 cases occur per million people, and most of those cases are in children aged 2–5 years. The cause of ALL remains largely unknown, although a small number of cases are associated with inherited genetic syndromes.† Both girls are suffering from anemia (low blood cell levels), fevers, bleeding, and are pale and thin. Dr. Ryder has decided to treat them as in- patients, keeping them in the hospital while treating them with a “thiopurine” drug called 6-mercaptopurine (6-MP) known to be highly effective in treating leukemia. Thiopurines are very similar to the regular purine nitrogen bases such as adenine and guanine that make up DNA and RNA. The only difference is that thiopurines have an extra sulfur group attached to them. They are similar enough to a regular purine base that our cells convert them to nucleotides (with the addition of a deoxyribose sugar and phosphate). These modified thioguanine nucleotides (TGN) are then incorporated into DNA.

The TGN nucleotides interfere with DNA replication and stop rapidly growing cells like cancer cells from further growth. Unfortunately, they also block the growth of other fast growing cells needed for good health, like the cells in the bone marrow that develop into erythrocytes (red blood cells) and leukocytes. As with

Pharmacogenetics: Using Genetics to Treat Disease*

 

 

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many drugs given as chemotherapy, it is important to give a high enough dosage to prevent cancer cells from replicating, while avoiding damage to the normal tissues. Too high a drug dose can be very toxic. Dr. Ryder knows that drugs are processed in various ways in the body. They must be absorbed by the blood, distributed throughout the body’s tissues, converted or transformed into forms that are easier to eliminate, and then removed from the body. Dr. Ryder gives both girls the same dosage of the drug before leaving the hospital for the night.

While making her rounds over the next few days, Dr. Ryder sees Laura’s vital signs plummet. Her anemia has worsened; her erythrocyte count is so low that her heart function could be compromised. Her fevers are spiking, and her breathing is becoming shallow and labored. She is not eating and is being hydrated intravenously. Her condition is life-threatening. In contrast, Beth’s anemia has decreased, she is free of fever, and is actually showing signs of an appetite and boredom, good indicators of improved health. Dr. Ryder had not anticipated that the drug could act so differently in two individuals. Even as she looks at Beth’s chart, she can picture Laura’s body struggling to hold its own just two private rooms away. Dr. Ryder knows she must find out why her patients are responding so differently. But where should she start, and will she find an answer in time to help Laura?

Questions 1a. Suggest a reason why the drug might affect the two girls differently.

1b. What tests might Dr. Ryder order to determine why the two girls are reacting as they are to the drug? Provide two or three appropriate examples of tests.

 

 

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Part II – Enzyme Activity Dr. Ryder learns that the difference in patient reaction to the drug probably has something to do with how the drug is naturally metabolized in the body to be removed as waste. After searching the scientific literature, she learns that the drug 6-MP can either be converted to the active form, TGN nucleotides, or can be inactivated with the help of the TPMT enzyme (thiopurine methyltransferase). Within each patient who takes the drug, both processes are occurring and they compete with each other.

Figure 1. Flow Chart Flow chart showing activiation and inactivation paths of the drug 6-MP.

 

 

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Since the therapy aims to harm rapidly replicating cells without overly impacting normal ones, it is important that excess drug is inactivated. Dr. Ryder decides to see how levels of the TPMT enzyme activity might vary between people.

She reviews the research papers that have been published about the TPMT enzyme and finds an interesting graph. From a study of 298 randomly selected Caucasian individuals, researchers found the following levels of TPMT enzyme activity:

Figure 2. Simplified Results. Simplified bar graph showing results from a study of 298 randomly selected Caucasian patients.

Questions 2a. If Dr. Ryder had 10 Caucasian patients in the next month, how many would you predict to have each

of the TPMT enzyme activity levels, based on the graph above?

Low:

Medium:

High:

Would you expect the actual/observed number of patients to be different? Why might there be differences?

2b. Each individual inherits two copies of the gene for the enzyme, one from each parent. Dr. Ryder suspects that variation in enzyme activity level is controlled by two different versions (alleles) of that gene. Does this graph (and the number of phenotypes) suggest that enzyme activity levels are based on a dominant/recessive or a codominant pattern of inheritance? Explain your answer.

Source: Simplified graph patterned after the top panel of Figure 2 in: Weinshilboum, R.M., and S. Sladek (1980) Mercaptopurine pharmacogenetics: Monogenic inheritance of erythrocyte thiopurine methyltransferase activity. American Journal of Human Genetics 32:651–662.

 

 

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2c. Which bar (low, medium, or high) represents individuals who might be homozygous for a “low enzyme activity’” version of the gene? Which bar represents individuals who might be homozygous for a “high enzyme activity” version of the gene? Which bar represents heterozygotes?

2d. Answer the question: “How does enzyme activity level vary among the patients examined?” In your answer, be sure to include supporting data from the graph above. Explain how these data support your conclusion.

2e. Challenge question: The actual graph (below) showed much more detail. Why do you think that there is more variation between patients than shown in the simplified graph?

Figure 3. Histogram RBC TPMT frequency distribution histogram for 298 randomly selected Caucasian subjects.

Source: Histogram drawn after top panel of Figure 2 in: Weinshilboum, R.M., and S. Sladek (1980) Mercaptopurine pharmacogenetics: Monogenic inheritance of erythrocyte thiopurine methyltransferase activity. American Journal of Human Genetics 32:651–662.

 

 

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Part III – TPMT Enzyme Activity Levels Dr. Ryder tested Laura, who was very sick, and found that her TPMT enzyme activity level was extremely low.

Question 3a. Why would individuals with the lowest level of enzyme get the sickest when they take the drug?

Suggest one possible reason.

Investigating further, Dr. Ryder decides to look at drug levels in many patients who are all receiving the same standard doses of the thiopurine drug and compare them to enzyme levels. When she compares the level of thioguanine nucleotides (TGN) created by the thiopurine drug to the body’s level of TPMT enzyme in patients, this is what she finds:

Figure 4. Scatter Plot of TGN vs. Enzyme Activity Thioguanine nucleotide concentrations and TPMT enzyme activity levels in 95 Children with Acute Lymphoblastic Leukemia (ALL) who were being treated with standard doses of thiopurine drugs.

Source: Modified from Lennard L., J.S. Lilleyman, J. Van Loon, and R.M. Weinshilboum (1990) Genetic variation in response to 6-mercaptopurine for childhood acute lymphoblastic leukaemia. Lancet 336:225–229.

Question 3b. Describe the relationship between TPMT enzyme activity levels and TGN levels. Be sure to include

supporting data from the graph.

 

 

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Part IV – Putting It All Together From her research, Dr. Ryder hypothesized that patients such as Laura (who became very sick upon receiving the drug) have very high / low TPMT enzyme activity and therefore very high / low levels of TGN nucleotides at normal doses. They easily became sick from the effects of the drug, and could even die. These patients are homozygous / heterozygous for the version of the gene encoding high / low enzyme activity. A better drug dose for these patients is 1/10th the level of other patients.

Patients such as Beth with high / low TPMT enzyme activity had high / low levels of TGN nucleotides. These patients would do well with the drug, and in some cases might even need a larger-than-normal dosage for the treatment to be most effective. These patients were either homozygous for the version of the gene encoding high / low enzyme activity, or were heterozygous.

Based on the graph in Part II, about 10% of the Caucasian population is homozygous / heterozygous.

Question 4. In the paragraphs above, circle the correct answer (high or low, heterozygous or homozygous).

 

 

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Part V – SNPs and TPMT DNA techniques reveal TPMT gene is located on chromosome 6, is about 34 kilobases in length (34,000 DNA bases), and has 8 exons. An exon is a region of a gene that is present in the final functional transcript (mRNA) from that gene. The diagram below shows a representation of the TPMT gene, showing the exons as boxes. The first “wild type” is the most common version. In our case, the second version of the TPMT gene is associated with low enzyme activity (TPMT*3A) and has two single nucleotide polymorphisms (SNPs), or changes in single DNA nucleotide bases (from “G” to “A” in one case and from “A” to “G” in another) that result in different amino acids being inserted in the enzyme. This, in turn, affects the enzyme’s function. Over 20 different gene variants have been found, three of which are shown below.

Figure 5. Selected Human TPMT Alleles. The wild-type human TPMT allele (TPMT*1) and variant alleles TPMT*3A, TPMT*3B, and TPMT*3C. Rectangles represent exons, with black coding areas and white untranslated regions.

Source: Weinshilboum, R. (2001) Thiopurine pharmacogenetics: Clinical and molecular studies of Thiopurine Methyltransferase, American Society for Pharmacology and Experimental Therapeutics 29:601–605. Available online at http://dmd.aspetjournals.org/. This case is based on this article.

Questions 5a. Dr. Ryder now has the ability to conduct a SNP genetic test on her patients to determine what level

of drug they should get. A new patient on the ward, Kevin, is homozygous for TPMT 3A*. The graph shown in Part III is reproduced on the next page. Circle the area of the graph that might likely corresponds to Kevin’s TGN and enzyme activity levels. Explain why you circled that region.

 

 

“Pharmacogenetics” by Jeanne Ting Chowning Page 9

Case copyright held by the National Center for Case Study Teaching in Science, University at Buffalo, State University of New York. Originally published February 4, 2010. Please see our usage guidelines, which outline our policy concerning permissible reproduction of this work. Title block illustration, licensed, ©Scott Maxwell | Dreamstime.com.

5b. What level of the drug (low, medium, or high) should Dr. Ryder give him? Explain your answer.

5c. In your own words, summarize how knowing someone’s TPMT DNA sequence could be used to determine what kind of medical care they should receive.

Postscript Dr. Ryder responded quickly to Laura’s drug reaction. She discontinued the drug while alternate treatment regimens were explored, and Laura’s condition began to improve.

 

 
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BI101 Unit 1 Experiment

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  • Read through the introductory materials below.
  • Open the Unit 1 Experiment Answer Sheet and complete the following Experiment exercises this unit:
    • Experiment 1 Exercise 1 – The Scientific Method (~30-45 min)
    • Experiment 1 Exercise 2A – pH of Common Materials (~30-45 min)
    • Experiment 1 Exercise 2B – pH and Buffers (~45-60 min)
  • Save your completed Unit 1 Experiment Answer Sheet and submit it no later than Sunday midnight CT.

The Scientific Method – Introduction

The Scientific Method is the basis for almost all scientific research. If you click on the Unit 1 Overview page, you can read about how the Scientific Method is conducted. You can also read about the process in your book on pp 14-17. One area of confusion often involves the difference between a hypothesis and a prediction. This is because many people use these terms interchangeably, but in fact, they are different. Here is how your book discerns the two:

Hypothesis – an answer to a question or explanation of an observation (p 14).

Prediction – an expected outcome if our hypothesis is correct; often worded as “if…then” (p15).

The purpose of this first exercise is to have you use the Scientific Method yourself. We will use the following web site. Be sure that you can access it and use it:

Bowers, N. 2013. Scientific Method Exercise (Links to an external site.)
When you are ready to begin, use the instructions in the Unit 1 Experiment Answer Sheet and work through the exercise.

pH of Common Materials – Introduction

This unit we are also learning about some of the chemistry that is important in biological systems, such as pH. Be sure you have read pp 32-33 in your book and our online lecture this unit before beginning this exercise. The pH scale ranges from 0 to 14; a pH less than 7 is considered acidic and a pH greater than 7 is basic. The pH scale is logarithmic, which means that a solution with a pH of 3 is ten times more acidic than a solution with a pH of 4 and a hundred times more acidic than a solution with a pH of 5.

Acids and bases are not necessarily a bad thing. Many of the materials that we handle and eat and drink everyday vary in pH. Some of these materials are safe to handle, such as “weak” acids (e.g., soda, coffee). Stronger acids (e.g., battery acid) and bases (e.g., ammonia) can be quite caustic and damaging. One way to measure the pH of liquids is to use pH indicator paper; paper that turns a particular color depending on the pH of the solution. Anyone with a swimming pool or hot tub is probably familiar with such paper.

When you are ready to begin, open the Unit 1 Experiment Answer Sheet and follow the instructions to complete this exercise.

Buffers – Introduction

As you saw in the previous exercise, the pHs of common solutions vary across the pH scale! Yet our body is constrained to work within a very narrow pH range. Small changes in pH can alter the function of biologically important molecules such as enzymes, by breaking hydrogen bonds and denaturing these proteins. For this reason, in most organisms (such as ourselves), pH is very closely regulated. pH can be kept relatively constant by the use of buffers, chemicals which can absorb or release hydrogen ions to maintain a relatively steady pH.

In most vertebrate animals, blood pH must be maintained between 7.35 and 7.45. There are several biological buffers that work to maintain this pH; one of the more important being the carbonic acid – bicarbonate system:

H2O + CO2 <–> H2CO3 <–> H+ + HCO3-

In the reactions above, the double headed arrows indicate that each step is reversible. If carbon dioxide (CO2) levels increase in our blood, it can combine with water to form carbonic acid (H2CO3), which can break down to form bicarbonate (HCO3-) and hydrogen ions. This would shift the pH towards the acidic end. If the acidity levels become too high, the whole process will reverse, such that hydrogen ions are removed and carbon dioxide is produced; thereby shifting the pH towards the alkaline end. This is only one example of a biological buffer; there are several other systems involved, but they all operate in a similar manner.

The purpose of this exercise is to help you understand the chemistry of buffers. Be sure that you have read through the material on pp 32-33 in your book and this unit’s online lecture on The Chemistry of Life. For this exercise, you will use the following website (be sure your speakers are on):

McGraw-Hill Education. No date. Buffers Animation. (Links to an external site.)

You may need to download and install a plugin to use this simulation, so test this simulation early in the unit in case you run into problems. When you are ready, open the Unit 1 Experiment Answer Sheet and follow the instructions there to complete this exercise.

WEEK 1 EXPERIMENT ANSWER SHEET Please submit to the Week 1 Experiment dropbox no later than Sunday midnight.

SUMMARY OF ACTIVITIES FOR WEEK 1 EXPERIMENT ASSIGNMENT

· Experiment 1 Exercise 1 – The Scientific Method

· Experiment 1 Exercise 2A – pH of Common Solutions

· Experiment 1 Exercise 2B — pH and Buffers

Experiment 1 Exercise 1: The Scientific Method

After viewing following video, answer the questions that follow:

Bowers, N. 2013. Scientific Method Exercise http://www.youtube.com/watch?v=8S7N_1xnYEE&feature=youtu.be

1. Write out four biological observations you made as you watched the video. Be specific about what you saw. These observations might deal with the habitat, season, flora, fauna, behaviors and interactions (2 pts).

2. Choose one or two of the observations above and write two questions you have regarding what you observed (2 pts).

3. Based on your observations or questions write two possible hypotheses that might explain your observation and/or answer your question (2 pts).

4. Write one prediction based on each hypothesis listed in Q#3 (2 pts).

5. What additional information might you need in order to design and conduct an experiment to test that one of your hypotheses (2 pts)?

Experiment 1 Exercise 2A: pH of Common Solutions

Be sure that you have completed your text book readings, have read through the online lecture and have read the introductory material for the Week 1 Experiment before starting. First, answer the following questions:

Questions

1. What is the definition of an acid? Your definition should include more than just a pH range. Provide one example of an acid. Cite your sources. (2 pts).

2. What is the definition of a base? Your definition should include more than just a pH range. Provide one example of a base. Cite your sources. (2 pts).

Procedure

A. Using your textbook, online lecture or other source, fill in Table 1 below. Be sure to complete your predictions BEFORE you look up the actual pH values.

B. Be sure to provide complete citations for the sources used to determine the actual pH values.

Table 1. Predicted and actual pH values and your explanations. You are only required to complete the first six; the others are optional. Use your textbook, online lecture or other source to determine the actual pH values (6 pts).

 

 Substance Predicted pH Explanation for Prediction Actual pH
1 Lemon juice      
2 Stomach acid      
3 Oven cleaner      
4 Antacid      
5 Pure water      
6 Orange juice      
Optional additional solutions
7 Sea water      
8 Vinegar      
9 Shampoo      
10 Soft drinks      
11 Tomatoes      
12 Battery acid      

Questions

1. Which of your substances tested are considered an acid (1 pts)?

2. Which of your substances tested are considered a base (1 pts)?

3. What surprised you most about your results in this activity (1 pts)?

Experiment 1 Exercise 2B: Buffers

Before beginning, answer the following question:

Question

1. What is a buffer and briefly, how do they work? Cite your source (2 pts)?

Procedure

Watch the following simulation and answer the questions after watching.

https://www.youtube.com/watch?v=ZLKEjXbCU30

Questions

2. Why does the green bar in the graph drop? Why does the purple bar in the graph rise? Explain what is occurring chemically (4 pts).

3. In the simulation shown, what happens to the pH in the beaker when HCl is added? How do you know this based on what you see in the graph (2 pts)?

4. What will happen to the pH if HCl is added after all of the acetate is used up? (1 pts)?

5. What is formed when sodium hydroxide is added and how does this affect the pH (4 pts)?

 

Week 1 Experiment Grading Rubric

Component Expectation Points
Experiment 1 Exercise 1 Demonstrates an understanding of the Scientific Method and an ability to apply it (Table 1, Questions 1-3) 10 pts
Experiment 1 Exercise 2A Demonstrates an understanding of pH and how it applies to your everyday life (Table 2, Questions 1-5). 13 pts
Experiment 1 Exercise 2B Demonstrates an understanding of pH and the effect of buffers (Questions 1-5) 13 pts
TOTAL  

 36 pts

Updated August 2017

 
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BioChemistry Test

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Question 1.1. Rank butane (CH3CH2CH2CH3), butanoic acid (CH3CH2CH2COOH), and pentane (CH3CH2CH2CH2CH3) in order of increasing boiling point. (From lowest to highest.) (Points : 3)

butane < butanoic acid < pentane        butane < pentane < butanoic acid        butanoic acid < pentane < butane        pentane < butanoic acid < butane

 

Question 2.2. Choose the equilibrium constant that indicates the greatest relative amount of reactant concentration at equilibrium. (Points : 3)

1.1 x 10–7        2.3 x 107        6.7 x 102        8.3 x 10–2

 

 

Question 3.3. Which of the following is the conjugate acid of NH3? (Points : 3)

NH2-        NH4+        HNO3        H3O+

 

 

Question 4.4. What volume of 0.200 M HCl is required to completely neutralize 50.00 mL of 0.150 M KOH? (Points : 3)

7.50 mL        50.0 mL        66.7 mL        37.5 mL

 

 

Question 5.5. The fluid mosaic model  proposes that (Points : 3)

membranes can move like a fluid.        proteins are embedded into the cell membrane.        materials that are fluid move across a membrane.        the composition of membranes includes a mosaic fluid

 

 

Question 6.6. The IUPAC name of the molecule below is                                        (Points : 3)

hydroxyl -2,4-dichlorocyclohexene        3,4-dichlorophenol        2,4-dichlorophenol        1,3-dichlorophenol

 

 

Question 7.7. Which of the following is the conjugate base of the acid, carbonic acid?  (Points : 3)

H2CO3        H2O        H3O+        HCO3–

 

 

Question 8.8. How many alkane constitutional isomers exist with the formula C5H12? (Points : 3)

2        3        4        more than 5

 

 

Question 9.9. The side chain of the amino acid tyrosine is shown here. The side chain is classified as ___. (Points : 3)

nonpolar        polar-acidic        polar-basic        polar-neutral

 

 

Question 10.10. Which of the following lipids is not derived from cholesterol? (Points : 3)

progesterone        thromboxane        cortisol        testosterone   51.Which is an α-amino acid?   *a)  b)  c)  d)

 

 

Question 11.11. Antacids may contain which ion to reduce acidity? (Points : 3)

Na+        CO32–        Al3+        Cl–

 

 

Question 12.12. In which of the following levels of protein structure can hydrogen bonding NOT play a role? (Points : 3)

primary        secondary        tertiary        quaternary

 

 

Question 13.13. What is the pH of a solution in which [H3O]+ is 2.2 x 10-12 M? (Points : 3)

2.34        4.54 x 10-3        11.66        8.42

 

 

Question 14.14. What level of protein structure is not disturbed by denaturing? (Points : 3)

tertiary structure        primary structure        secondary structure        quaternary structure

 

 

Question 15.15. The pH of a 1.25 x 10-3 M NaOH solution is: (Points : 3)

2.90        7.00        11.1        3.10        10.9

 

 

Question 16.16. What is the concentration of [H3O+] in an aqueous solution when the [OH-] is 5.2 x 10-9 M? (Points : 3)

1.9 x 10-6 M        5.7 M        1.0 x 10-14 M        9.8 x 10-9 M

 

 

Question 17.17. The element found in the center of the heme prosthetic group is ___. (Points : 3)

iron        sulfur        nitrogen        carbon

 

 

Question 18.18. The Ka for the reaction of acetic acid and water shown below is 1.8 x 10-5.   Which of the following statements is true at pH 7? (Points : 3)

there is much more acetic acid than acetate ion        there is more acetate ion than acetic acid        the concentration of acetate ion is equal to that of acetic acid        the pH is lower than pKa of acetic acid

 

 

Question 19.19. Which of the following statements is true about alkanes? (Points : 3)

alkanes contain polar bonds        alkanes are attracted to one another by London forces        alkanes are polar molecules        alkanes are unsaturated hydrocarbons

 

 

Question 20.20. The structure of glycerophospholipids contains (Points : 3)

a phosphate group, glycerol, three fatty acids, and a sugar molecule.        a phosphate group, glycerol, two fatty acids, and an alcohol molecule.        a phosphate group, a cyclic carbon ring, and variable numbers of fatty acids.        a phosphate group, a carbohydrate molecule, an alcohol, and fatty acids.

 

 

Question 21.21.  Kw, the equilibrium constant for the ionization of water by the equation below, is 1.0 x 10-14. What does that mean when we are considering pure water?  (Points : 3)

More ions exist than water molecules.        The majority of the molecules present are in the form of H2O.        The amount of water is the same as the amount of the ions present.        There will always be more hydronium ions present than water at equilibrium.

 

 

Question 22.22. Carbon must form how many bonds? (Points : 3)

1        2        3        4

 

 

Question 23.23. What is the function of nonsteroidal anti-inflammatory drugs (NSAID)? (Points : 3)

To interrupt the production of prostaglandins from arachidonic acid.        To interfere with the production of anabolic steroids.        To facilitate the production of cyclooxygenase.        To stimulate the production of leukotrienes.

 

 

Question 24.24. You produce 500 mL of a 0.001 M HClO4, which ionizes completely in water. What is the pH you should expect? (Points : 3)

pH = 0.5        pH = 3.0        pH = 2.7        pH = 500

 

 

Question 25.25. The α-helix and β-pleated sheet are both forms of the ___ structure of proteins. (Points : 3)

primary        secondary        tertiary        quaternary

 

 

Question 26.26. The ethylammonium ion, CH3CH2NH3+ has a pKa of 10.81. It reacts with water to form ethylamine, CH3CH2NH2 and H3O+ as shown below. Which of the following statements is true at pH 7? (Points : 3)

ethylammonium ion predominates        ethylamine predominates        the concentration of ethylamine equals that of ethylammonium ion        the pH is higher than pKa of the ethylammonium ion

 

 

Question 27.27. Which of the following is the conjugate acid of the bicarbonate ion, HCO3-? (Points : 3)

H2CO3        CO32-        CO2        H3O+

 

 

Question 28.28. A solution in which the concentration of H+ is greater than the concentration of OH- will (Points : 3)

have a pH greater than 7.0 and be basic.        have a pH less than 7.0 and be basic.        have a pH greater than 7.0 and be acidic.        have a pH less than 7.0 and be acidic.

 

 

Question 29.29. Whenever an equilibrium constant, Keq, has a value greater than 1, which of the following statements is true at equilibrium? (Points : 3)

The concentration of reactants is greater than the concentration of the products.        The concentration of products is the same as the concentration of reactants.        The concentration of the products is greater than the concentration of the reactants.        Relative composition of reaction mixture cannot be predicted.

 

 

Question 30.30. The term commonly used for a chain of amino acids 100 units long is ___. (Points : 3)

peptide        oligopeptide        polypeptide        centapeptide

 

 

Question 31.31. Which material would be effective for neutralizing a minor acid spill? (Points : 3)

soap solution        vinegar solution        baking soda        household ammonia

 

 

Question 32.32. One characteristic of basic solution is that (Points : 3)

the solution would turn litmus red.        the solution would have a slippery feel to it.        the solution would have a sour taste.        the solution would dissolve some metals.

 

 

Question 33.33. Give the correct IUPAC name for the following molecule:  (Points : 3)

3, 4-Dimethylpentane        2,3-Dimethyl heptane        2,3-Dimethylpentane        1,1,2-Trimethylpentane

 

 

Question 34.34. A Ka can be calculated for some chemical reactions. The Ka is (Points : 3)

the Keq for the reaction to the right.        the Keq for the reaction to the left.        the Keq for the dissociation of an acid.        the pH of a very weak solution.

 

 

Question 35.35. The equation: has the following equilibrium constant expression. (Points : 3)

 
 
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Lab 6. Energy use

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Lab 6: Follow the instructions and complete the assignment below. Submit your answers through the Lab 6 Assignment on Blackboard.

Lab 6 1

Lab 6. Energy use

In this week’s lab, you will visualize metabolism in a living organism, evaluate some scientific claims regarding metabolic processes, and use your own scientific and mathematical thinking skills to personally evaluate a “popular” weight loss mantra. Part 1: Sugar Metabolism in Yeast As we are learning this week, living organisms harvest energy from “food” through cellular processes contributing to an organisms “metabolism”. These processes involve the transfer of energy from of carbon based molecules (that were originally produced during photosynthesis) to a more readily useable form (most commonly, ATP), and the carbon is released as waste. This part of the lab will demonstrate the importance of sugar for the metabolic processes of the fungal organism, Saccharomyces cerevisiae, commonly known as baker’s yeast. Yeast are a single-celled type of fungi that humans use and interact with every day. Beneficial applications of these organisms are diverse, ranging from cooking to bioremediation, while some species are also responsible for causing illnesses like athlete’s foot and ringworm. Interestingly (and fortunately for us), yeast can effectively harvest energy from sugar in the absence of oxygen, and this is precisely what we will be observing today. This process is somewhat similar to the aerobic respiration that our (human) cells undergo, in that both processes break down sugar molecules releasing carbon waste; however, no oxygen is required for fermentation. This is why yeast are sometimes called anaerobic organisms. Materials: for this activity, you will need:

 Ruler, able to measure centimeters.

 Marker/tape for labeling

 4 sandwich or quart (or larger) size sealable ziploc bags (if you are able to splurge on bags that you trust will seal, versus the cheaper ones with questionable sealing abilities, do so- it will be worth it).

 4 packages Bakers Yeast (available at any grocery store in the baking aisle)

 Table Sugar (~2 tablespoons or 2 sugar packets; sugar substitute will not work)

 Warm water (4 cups)

 1 tbs measuring spoon for measuring sugar

 1 cup measuring cup for measuring water Experimental Set Up: A. Label your Ziploc bags. Use caution; do not tear or poke a hole in the bag(s)

1: Yeast + Water 2: Yeast + Water 3: Yeast + Water + Sugar

 

 

Lab 6: Follow the instructions and complete the assignment below. Submit your answers through the Lab 6 Assignment on Blackboard.

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4: Yeast + Water + Sugar B. Add 1 package of yeast to each ziploc bag. C. Add 1 tablespoon of sugar to yeast in ziploc bags 3 and 4 only. D. Carefully add 1 cup of warm water to each ziploc bag (one at a time is fine).

Eliminate as much air from the bag as possible before sealing and mix carefully.

 Try to dissolve all the solid clumps in the water, but be gentle with the yeast, and try not to damage the bags.

 The less air you have in the bags at this point, the better your results will be. See image:

 Manage your time carefully here, you don’t want too much time to go by between activating (adding the water) the different treatments.

E. Start your timer and check the seal of each bag for good measure (leaks = messy clean up).

F. Measure the height of the Ziploc bag in centimeters (cm). To do this, hold the ruler up

vertically next to the ziploc bag, and record how “tall” the bag is; the distance between the top of the bag and the bottom (surface of the table is fine). Record your measurement in the provided Yeast Metabolism Data table (below). Also note in the table any observations you have about each treatment (color, bubbles, anything else you notice). This is your time 0 measurement.

G. Every 5 minutes for 45 minutes, gently mix solutions inside bags, and repeat measurements.

 Use caution as you approach and pass 45 minutes; the bag may burst (= messy!)

H. After the final, 30-minute, measurement, calculate the change in Ziploc bag height for each treatment by subtracting time 0 (starting) height measurement from the time 30 height measurement (of the same sample). The difference between these values gives you actual increase in height for each treatment. For example, if your time 0 height was 2cm, and your time 30 height was 10 cm, that treatment would have increased by 8 cm. Fill these values in the Change in Height row (labeled H) of the Yeast Metabolism Data table, below.

I. Determine the average change in height for each condition Yeast without or with sugar. To do this, add the values determined for the Change in Height for treatments 1 and 2, and divide this number by 2. This is your average change in height for the minus sugar condition. Repeat this step for the values obtained for treatments 3 and 4 to determine the average plus sugar height change. Fill these values in the Average Height Change row (labeled I) of the Yeast Metabolism Data table, below.

 

 

 

Lab 6: Follow the instructions and complete the assignment below. Submit your answers through the Lab 6 Assignment on Blackboard.

Lab 6 3

Note: this experiment can also be performed with balloons attached to the top of ~16oz small spout plastic bottles, as seen in the image (20oz soda or water bottles work well, after they’ve been rinsed thoroughly of course). The visual effect of this set up is much better than with Ziploc bags, but more materials are needed (4 balloons, 4 bottles, funnel for transporting ingredients to bottles, etc….) if you are able to/want to repeat the experiment this way, I highly recommend it (it’s a lot more fun). Show your friends and family your new party trick  Yeast Metabolism Data:

Expired Time

Treatment 1: Yeast+Water

Treatment 2: Yeast+Water

Treatment 3: Yeast+Water+Sugar

Treatment 4: Yeast+Water+Sugar

Height in cm

Observations Height in cm

Observations Height in cm

Observations Height in cm

Observations

0 minutes

 

 

5 minutes

 

 

 

 

10 minutes

 

 

 

 

 

15 minutes

 

 

 

 

20 minutes

 

 

 

 

 

25 minutes

 

 

 

 

30 minutes

 

 

 

 

35 minutes

 

 

 

 

 

Lab 6: Follow the instructions and complete the assignment below. Submit your answers through the Lab 6 Assignment on Blackboard.

Lab 6 4

40 minutes

 

 

 

 

45 minutes

 

 

 

 

(H) Height Change:

Treatment 1: Yeast+Water

Treatment 2: Yeast+Water

Treatment 3: Yeast+Water+Sugar

Treatment 4: Yeast+Water+Sugar

(I) Avg Height Change

Yeast (minus sugar): Yeast + Sugar:

When you are finished, answer the following questions:

1. Describe your observed results of the yeast metabolism experiment (include observations and average change for each treatment)? Were these the results you were expecting? Is your average an accurate representation of your treatment data? Why/why not? 2. Based on what you learned this week and the conditions that the yeast cells were in during this experiment, which metabolic process did the yeast undergo? What gas was produced? How do you know? Can humans carry out this process, and if so, what purpose does it serve in human cells? 3. If you were to compare the results of this experiment from several different people, assuming that they all implemented the procedure in the exact same way, would you expect each person to get exactly the same results? Why or why not? In your answer discuss possible sources of variation in this experiment. 4. The sugar that was added to the ziploc bags represents the “food” source for the yeast. Where did the energy that the yeast extracted from the sugar originally come from? Explain how you know this. 5. When you make bread, if you just mix flour, sugar and water, the dough does not rise, and the bread will be flat and hard. If you include yeast in the bread dough, then the dough rises and the bread is bigger and fluffier. Use your results from the yeast metabolism experiment to explain how the yeast helps the bread dough to rise.

6. Discuss how this yeast metabolism experiment relates to the material that we learned this week (and previous weeks!). Use specific examples.

 

 

 

Lab 6: Follow the instructions and complete the assignment below. Submit your answers through the Lab 6 Assignment on Blackboard.

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Part 2: Is Lost Weight Really Lost? In the next part of this week’s lab, we will read about some research that used mathematical evidence to answer this very question, but also collected some shocking data about what the general public understands about cellular respiration and human metabolism. Below you will find links to read the original, primary, research article, and a few additional summary articles generated for the popular media based on the original. Original Research Article: http://www.bmj.com/content/bmj/349/bmj.g7257.full.pdf Take some time to review the original article first. Don’t be intimidated. For a scientific article, the language is fairly easy to understand for a non-scientist. That being said, don’t worry if you don’t understand every word. Take notes while you read and try to get the general idea of:

 What is the main point of the study? What was the study trying to find out?

 What are the main conclusions, their results/findings?

 How does the study apply to you, and what we’ve learned this week (and this semester)? After you’ve familiarized yourself with the original article, follow the other links to review the 6 summary articles. As you are reading each, take notes. Consider/evaluate each of the following.

 What is/are the main point/s of the article?

 Are the main points of the article consistent with the original research study? Is the article appropriately using information from the original study, or skewing it/making a new point?

 Do you notice anything questionable about the summary article, for example in terms of disclosures, conflicts of interest, echo chamber, etc…. remember our Lab 1materials!

 Is the source reputable? Remember our Week 1 materials! Summary Article 1: https://www.medicalnewstoday.com/articles/287046.php

Summary Article 2: https://www.scientificamerican.com/article/when-you-lose-weight-wher/

Summary Article 3: https://www.npr.org/sections/health-shots/2014/12/16/371210831/when-

you-burn-off-that-fat-where-does-it-go

Summary Article 4: https://www.sciencedaily.com/releases/2014/12/141216212047.htm

Summary Article 5: http://theconversation.com/when-we-lose-weight-where-does-it-go-91594

Summary Article 6: https://www.beachbodyondemand.com/blog/where-does-fat-go-when-you-

lose-weight

When you are finished, answer the following questions: 7. Compared to the original metabolism research article, which summary article do you find to be the most accurate? Which summary article do you find to be the least accurate? Explain your answer, providing at least 2 valid reasons why for each.

 

 

Lab 6: Follow the instructions and complete the assignment below. Submit your answers through the Lab 6 Assignment on Blackboard.

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8. Which metabolism summary article source (publisher) do you find to be the most reputable/trustworthy? Which summary article source (publisher) do you find to be the least reputable/trustworthy? Explain your answer, providing at least 2 valid reasons why for each. 9. Based on the original metabolism research study, when you lose weight, how does the matter leave your body? Identify in what all the forms that the matter is in as well as the percent of each form. With your response, state which article(s) you used to answer and why you chose to use this article as your reference. 10. It is several years in the future, and you are home visiting family for Thanksgiving. During Thanksgiving dinner, your brother is bragging about some of his recent weight loss accomplishments. He says “since he’s shed these 45lbs, that’s 20kg you know, I have all this extra energy”. He takes it even further, saying “as the weight comes off, it transforms right into energy!”. Based on the original research study, explain why this belief may seem logical, but is in fact, wrong. Include in your answer evidence from the original study that illustrates that the majority of people are incorrect in this assumption (hint: look at the figures). 11. It is several years in the future, and you are home visiting family for Thanksgiving. During Thanksgiving dinner, your brother is bragging about some of his recent weight loss accomplishments. He says “since he’s shed these 45lbs, that’s 20kg you know, I have all this extra energy”. He takes it even further, saying “as the weight comes off, it transforms right into energy!”. Based on the original research study, offer your brother a better, scientifically and quantitatively accurate, explanation to his observed phenomenon. Include numerical, quantitative data specific to your brother’s case to support your argument. For this, you must consider how much weight he has lost and based on the article, tell him exactly where that weight went. 12. After completing this week’s course material, you are talking with a friend, who is also taking this class. Your friend mentions that they find it super interesting how a simple, single celled organism, such as yeast can function so similar to us (only in certain ways of course). You ask what they mean, and they say “Well, if you think about it- in the yeast experiment we just did, they “exhaled” the carbon-based product of metabolism, just like we do!” Is your friends statement correct? Why/why not?

Part 3: Is it Really That Simple? It seems obvious, especially after viewing the summary articles in Part 2 of this lab, that we (humans) tend to have a fixation (no pun intended) on diets, fat, and weight. New diets (or lifestyle programs, if we want to use more current terms) seem to come out, one right after another, each claiming to be the next best way to provide quick, permanent, weight loss. However, the researchers behind the original article that we read in Part 2 of this lab argue that weight loss simply represents a balance between intake an output of matter; that to lose weight, you must consume fewer calories than your body uses. The question we will answer in this part of our lab is, is it really that simple? Specifically, as you calculate your own metabolic

 

 

Lab 6: Follow the instructions and complete the assignment below. Submit your answers through the Lab 6 Assignment on Blackboard.

Lab 6 7

rate and compare it with your typical daily caloric intake, you will put the “eat less, move more” weight loss claim to the test. Before we begin, remember calories are a measurement of energy and because one calorie is a very small unit, food calories are usually measured in units of 1,000 calories, called kilocalories (abbreviated kcal). Also note, although we are limiting our range of study in this exercise to calories only, the skills and information that you will glean here are directly applicable and relevant. To determine your daily energy expenditure/consumption, or metabolic rate, you will incorporate two components: your basal metabolic rate (BMR) and additional calories expended (on top of the cell maintenance/survival processes). Let’s start with your basal metabolic rate (BMR). It is important to note that BMR varies according to the following components (and some others). This experimental procedure takes all these factors into consideration.

 Body style: a tall, thin person has a higher BMR than a short, stout person

 Age: the younger the person, the more likely it is that cell division is occurring; therefore, BMR is higher for younger persons than for older persons

 Sex: males have a higher BMR than females because males have a greater percentage of

muscle tissue
 
 A. To calculate your BMR, use the formula below that is most appropriate for your inherited

(chromosomal based) gender. To do this, you will also need the following information:

 Your weight in pounds (lbs)

 Your height in inches (in)

 Your age in years

Resources: http://www.height- converter.com/

 

Female: BMR = 655 + (4.354 X weight in lbs) + (4.569 X height in inches) – (4.7 X age in years) Male: BMR = 66 + (6.213 X weight in lbs) + (12.69 X height in inches) – (6.8 X age in years)

 

 

Lab 6: Follow the instructions and complete the assignment below. Submit your answers through the Lab 6 Assignment on Blackboard.

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My BMR = _____ kcal. Next, we will use the “activity multiplier” to determine your total caloric expenditure (actual metabolic rate).

To give you an idea how daily activity impacts overall metabolic rate, review the figure. This figure shows the time required to “burn” 4 different caloric values through 3 different activity levels. B. Multiply your BMR (determined in the previous step) by the appropriate activity factor from the list (below) to determine your total caloric expenditure (actual metabolic rate).

 sedentary (desk job, with little or no exercise) = BMR X 1.2

 lightly active (light exercise, 1-3 days/week) = BMR X 1.4

 moderately active (moderate exercise, 3-5 days/week) = BMR X 1.6

 very active (intensive exercise, 6-7 days/week) = BMR X 1.7

My total caloric expenditure (BMR times the selected activity multiplier) = _____ kcal. C. Determine the number of calories for all the food you consume in a single day.

 Select a typical day when you eat your normal number of meals (with fairly average food choices) and record everything that you eat (including amounts and brand names). Consider using the food diary provided below to keep your records.

 Use the following websites to look up food caloric values. You may also find caloric info for specific foods on the food product wrapping or on manufacturers website. Note that preliminary research comparing calorie “calculators” has identified these two within the most accurate (use caution with others). o https://www.webmd.com/diet/healthtool-food-calorie-counter o https://www.myfooddiary.com/?network=g&keyword=food%20calorie%20counter

&matchtype=p&device=c&devicemodel=&adgroup=1037681552&position=1t1&cre ative=273779895484&gclid=Cj0KCQjw45_bBRD_ARIsAJ6wUXREPZgR4ZO9L5ZnsHV H3wK5iNtSeppegjULpzoEDfJVb1QzsGmlhnEaAh3gEALw_wcB

 If you have trouble finding information, use your best estimate. My total caloric intake over the recorded 24-hour period was ______ kcal.

D. Calculate your energy balance as: total kcal consumed – total kcal expended = ____ kcal

E. Return to your actual metabolic rate (energy expenditure calculations), above and

recalculate what your total calorie expenditures would be if you increased your activity

 

 

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Lab 6 9

multiplier by one level (for example, from light to moderate activity). If you were already at the highest activity level, recalculate for one level lower. My updated caloric expenditure (BMR times the updated activity multiplier) = _____ kcal.

F. Use this updated metabolic rate to recalculate an updated (hypothetical) energy balance, as

updated energy balance = total kcal consumed – updated total kcal expended = ____ kcal Our last step in this part of our lab is too evaluate if our calculations make any (real) sense. G. Click the link; visit the website

https://www.choosemyplate.gov/MyPlatePlan to get your USDA recommended calorie intake values. Click start on the “Get Your MyPlate Plan” widget.

H. When prompted, enter/fill in your

 Age

 Sex

 Pregnant/Breastfeeding Status

 Weight (pounds)

 Height (feed/inches)

 Approximate level of physical activity.

I. Click calculate food plan to review recommended the number of calories that the USDA recommends you intake in order to achieve and maintain a healthy weight. How do these numbers relate to your metabolic rate calculations?

When you are finished, answer the following questions:

13. State and discuss your actual metabolic rate determination and your USDA MyPlate calorie recommendations. Were these consistent? Were they (either or both) what you expected? Why/why not? 14. Visit https://www.choosemyplate.gov/MyPlatePlan and determine how many calories are recommended by the USDA MyPlate program in order to achieve and maintain a healthy weight for a 27-year-old, genetic female, that weighs 145lbs, is 5 feet 7 inches tall. She is not pregnant or breastfeeding, and she is exercises lightly, walking for 30 minutes 1-3 days a week.

 

 

Lab 6: Follow the instructions and complete the assignment below. Submit your answers through the Lab 6 Assignment on Blackboard.

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15. Calculate the actual metabolic rate for a 50-year-old, genetic male, that weighs 230 lbs, is 6 feet 3 inches tall. He is very active, running or playing basketball for 45 minutes to an hour 6-7 days a week. 16. Based on this figure, approximately how long would it take to burn 1,000 kcal at rest, by walking, and while jogging? Explain your answer; how did you come to this conclusion? 17. Discuss the meaning and long-term (over time) implications of the energy balance we calculated in the metabolic rate experiment. If a person’s calculated energy balance was positive every day long-term, what effect would that have on body weight over time? If a person’s calculated energy balance was negative every day long-term, what effect would that have on body weight over time? If a person’s calculated energy balance was 0 every day long-term, what effect would that have on body weight over time? Explain your answer (why this would happen) for each situation.

18. How did your calculated energy balance change when you updated (went up or down) an activity level? If your goal was to gain weight, what changes could you make in your daily diet to improve your energy balance situation? If your goal was to lose weight, what changes could you make in your daily diet to improve your energy balance situation? 19. Based on calorie considerations alone, which dieting strategy should be more effective for weight loss: a low carb diet or a low fat diet (recall: Carbohydrates and proteins each contain 4 kcal/g and Fats contain 9 kcal/g)? Explain your answer. 20. Based on your metabolic rate data and calculations, explain why athletes often gain weight when they retire from sports.

 
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