biology181 i need complete asap

1. https://asu.instructure.com/courses/232655/files/112427116?wrap=1

2. Mission Memo:

Cell Biology Act 2

Background

What an incredible medical discovery we have made together! A contagious cancer is one of the rarest

diseases throughout the galaxy. If left untreated, the cancer will not only spread from the lungs to other

organs but will spread from sick gliders to healthy gliders.

Fortunately, we have collected the data to determine how the tumor cells differ from healthy cells. The

elevated concentration of Growth Factor L in the blood of spotted gliders provides a clue to the mutations

responsible for the cancer. We may be able to use this information to devise a treatment that targets

tumor cells.

Use the following questions to guide your work:

● Which receptors in the cell membrane bind Growth Factor L? (Appendix 1)

● Which proteins in the cytoplasm are activated when a receptor binds Growth Factor L? (Appendix

2)

● Should we treat the cancer of spotted gliders with a drug or a virus? (Appendix 3)

Universally, in your debt,

The AI

You have been asked to identify the cellular component contributing to the spotted gliders’ cancer

and chose a treatment.

Appendix 1

Which receptors in the cell membrane bind to

Growth Factor L?

Cancer—the uncontrolled growth of abnormal cells—results from a malfunction in a signaling pathway.

The figure below shows a signaling pathway that regulates cell division in spotted gliders.

When the signaling pathway is inactive, a protein called CDI2 is active and prevents the cell from dividing.

All other proteins (R1, KR1, KR2, KR3, and CDP1) are inactive form.

When the signaling pathway is in the active state, the following steps occur:

1) A signal (SR1) binds to a receptor (R1), activating this receptor through phosphorylation.

2) The active form of R1 or R2 binds and phosphorylates a kinase (KR1).

3) The active form of KR1 binds and phosphorylates a second kinase (KR2).

4) The active form of KR2 binds and phosphorylates a third kinase (KR3).

5) The active form of KR3 interacts directly with two proteins, CDP1 and CDI2. KR3 activates

CDP1, which enables CDP1 to promote rapid cell division. KR3 inactivates CDI2, preventing

CDI2 from slowing cell division.

When examining the spotted gliders, we discovered an elevated concentration of a second type of signal,

which Phygaran scientists called Growth Factor L (abbreviated as GF-L). According to my database,

GF-L only reaches these concentrations during the embryonic stage, early in the development of spotted

gliders, when cells rapidly divide.

By experimenting with some cells from a spotted glider, you discovered that GF-L binds to receptors in

the membrane of a tumor cell. We might presume that these receptors are the same as R1, which would

explain how GF-L promotes cell division (see Figure 1). However, after you left the Intergalactic Wildlife

Sanctuary, I analyzed the membrane of tumor cells and discovered a second type of receptor, R2, that

has a similar structure to R1. According to research conducted on Phygaris, spotted gliders usually

produce R2 as embryos when rapid cell division creates new tissues and organs. R2 is not usually

expressed in adult gliders.

We need to understand GF-L's role in the cancer of spotted gliders. First, we need to determine

whether GF-L binds to R1 or R2. This knowledge will help us identify the cause of the cancer.

We will follow three steps to answer the question, “Is Growth Factor L binding to Receptor 1 or 2?”

Step 1: Anticipate your analysis. Determine what you should observe if GF-L binds to R1, R2, both

receptors, or neither receptor. This step will help us identify the evidence needed to build an argument in

Step 3.

Step 2: Model the effects of GF-L on the activity of R1 and the activity of R2. Determine how the

presence of GF-L affects the activity of R1 and the activity of R2. This step gives us the evidence needed

to build an argument in Step 3, when we will conclude whether GF-L binds to R1, R2, both receptors, or

neither receptor.

Step 3: Weigh the evidence and conclude if GF-L binds to R1, R2, both receptors, or neither

receptor. Construct an argument to answer the question “Does GF-L bind only to R1, only to R2, both

receptors, or neither receptor?” Your argument should draw on your answers in Steps 1 and 2.

Figure 1, long description

Figure 1. The signaling pathway regulating cell division in spotted gliders. Left: The key defines the

signaling components, including the signaling molecule (SR1), membrane receptor (R1 or R2),

phosphorylated secondary messengers (KR1-KR3), and proteins regulating cell division (CDP1 and CDI2).

Center: When SR1 binds to R1 or R2, the receptor is activated, triggering phosphorylation of KR1-KR3.

KR3 then activates CDP1, which promotes rapid cell division and inhibits CDI2, which normally slows cell

division. Right: In the deactivated pathway, the receptor remains inactive due to the absence of SR1.

Without activation, KR1-KR3 are inactive, CDP1 remains inactive, and CDI2 stays active, slowing cell

division.

Step 1: Anticipate your analysis.

To construct a sound argument, one must anticipate the evidence needed to support a claim. In this

assignment, you will be asked to defend a claim about whether GF-L binds to R1, R2, neither receptor, or

both receptors.

We measured the activity of R1 and the activity of R2 in the absence and presence of GF-L. Higher

activity indicates that more receptors of a given type (R1 or R2) are active.

Let’s anticipate the evidence needed to support each of the potential claims.

1. Below are four pairs of plots, each depicting two linear models. In each pair of plots, the linear

model on the left shows the linear relationship between the categorical independent variable

(absence or presence of GF-L) and the average activity (%) of Receptor 1 (R1); the linear model

on the right shows the linear relationship between the categorical independent variable (absence

or presence of GF-L) and the average activity (%) of Receptor 2 (R2).

Match each pair of figures and their corresponding linear models with the claim they support.

Claims

- Claim 1: GF-L binds only to R1 in the cell signaling pathway.

- Claim 2: GF-L binds only to R2 in the cell signaling pathway.

- Claim 3: GF-L binds to R1 and R2 in the cell signaling pathway.

- Claim 4: GF-L does not bind to R1 or R2 in the cell signaling pathway.

Figure Pairs A-D, Long description

Figure Pairs A-D. The relative activity of Left: Receptor 1 (R1) and Right: Receptor 2 (R2) in the

absence or presence of Growth Factor L (GF-L). Filled circles (R1) and diamonds (R2) represent the

mean relative activity of each receptor.

Step 2: Model the effects of GF-L on the activity of R1 and the

activity of R2.

Excel tutorials:

● #9 Saving/Uploading Excel Files - Mac or #9 Saving/Uploading Excel files - Windows

● #15 Modeling a Linear Relationship with a Categorical Independent Variable;

● #16 Plotting Linear Model of Categorical Variable;

To learn how the presence of GF-L relates to the cancer of spotted gliders, we must discover how GF-L

affects the activities of receptors R1 and R2. We performed an experiment in which GF-L was added to a

tumor cell. From that experiment, I estimated the activity of R1 and R2 in the presence or absence of

GF-L. You must use these data to determine how GF-L affects the activities of each type of receptor.

The two conditions in this experiment—presence or absence of GF-L—represent categories rather than

continuous values. Therefore, you will need to use a linear model with a categorical independent variable

to predict the mean activity of a receptor in the presence or absence of GF-L.

A linear model with a categorical independent variable can be described as follows:

μ = aX + b

μ is the expected activity of a protein (%) for a given category;

a is the slope of the linear relationship between the category and the mean activity;

X is the categorical independent variable representing the presence or absence of GF-L;

b is the intercept of the linear relationship between the category and the mean activity.

This linear model appears identical to that used for a continuous independent variable. However, the

value of X for a categorical variable can be only 0 or 1, where 0 arbitrarily represents one category and 1

arbitrarily represents the other category. Scientists routinely code categories alphabetically; for example,

because "Absence of GF-L" comes alphabetically before "Presence of GF-L", we should code

observations in the former group as 0 and observations in the latter group as 1. From here on out, we

will code categories alphabetically, so observations in the "Absence of GF-L" will be coded as 0

and observations in the "Presence of GF-L" will be coded as 1. In science, the recoding of a

categorical variable as 0 or 1 is referred to as dummy coding.

The Dummy Code may look like this:

=IF(logical_test, [value_if_true], [value_if_false])

Or

=IF(categorical variable data column=“Absent”,0,1)

Example:

Imagine that someone observed the body mass of 5 mice from each of two populations, a northern

population and a southern population. How would we dummy code a variable to represent these two

categories (northern vs. southern)?

The example Excel Spreadsheet below illustrates the standard method of dummy coding a categorical

variable in Excel. The two categories of mice, northern and southern, have been coded as 0 and 1,

respectively.

For these data, you would calculate the slope, intercept, and standard deviation of the linear relationship

by entering the following functions in Excel:

Dummy Code:

=IF(A2:A11=”northern”,0,1)

Slope:

=SLOPE(B2:B11, C2:C11)

= -2.0 g

Intercept:

=INTERCEPT(B2:B11, C2:C11)

= 25.3 g

Standard deviation:

=STEYX(B2:B11, C2:C11)

= 2.2 g

A B C

1 Population Body mass (g) Dummy

Code

2 northern 25.9 0

3 northern 26.1 0

4 northern 23.8 0

5 northern 24.4 0

6 northern 26.1 0

7 southern 25.3 1

8 southern 26.9 1

9 southern 20.1 1

10 southern 21.1 1

11 southern 22.7 1

Therefore, the linear model is

μ = -2.0X + 25.3

where X equals 0 for northern mice and 1 for southern mice.

With this model, we can calculate the mean body mass of mice in each category. In each case, we enter

the value of X and solve for the mean of absent or present (μ).

To compute the mean body mass of a northern mouse, we enter a value of 0 for X:

μ = -2.0(0) + 25.3

= 25.3 g

Additionally, we can compute the mean body mass of a southern mouse by entering a value of 1 for X:

μ = -2.0(1) + 25.3

= 23.3 g

Both means have a standard deviation (σ) of 2.2 g.

Part 1 - Effect of GF-L on the Activity of Receptor 1 (R1)

Directions: For questions 2-8, download the “CB Act 2 Workbook” from your Canvas and refer to the

sheets titled “Q2-8 GF-L and R1.” This sheet contain the activity (%) of Receptor 1 (R1) in the absence or

presence of GF-L (sample size = 10 measurements per category, absence or presence of GF-L). Create

a column of dummy codes to represent the two conditions, with 0 representing the absence of GF-L and 1

representing the presence of GF-L. Use Excel for calculations, modeling, and graphing.

2. Calculate the slope of the linear relationship between the absence or presence of GF-L and the

activity of Receptor 1 (R1).

3. Calculate the intercept of the linear relationship between the absence or presence of GF-L and

the activity of Receptor 1 (R1).

4. Calculate the standard deviation of the linear relationship between the absence or presence of

GF-L and the activity of Receptor 1 (R1).

5. Calculate the mean activity of Receptor 1 (R1) in the absence of GF-L using μ = aX + b.

6. Calculate the mean activity of Receptor 1 (R1) in the presence of GF-L using μ = aX + b.

7. Use the sheet (tab) to create a plot of a linear relationship between the categorical independent

variable (absence or presence of GF-L) and the mean activity of Receptor 1 (R1). Your plot

should follow the formatting guidelines listed below.

Formatting Instructions

● Chart type: Line with Markers

● Quick layout: Layout 4

● Chart title: “Activity of R1 in response to GF-L”, Font = 20

● Y-axis title: “Activity of R1 (%)”; Font size = 16

● Y-axis numbers: Font size = 14

● Y- axis minimum = 0, maximum =100

● X-axis title: “Absence or presence of GF-L”; Font size = 16

● X-axis numbers: Font size = 14

● Line: No line

● Note: Make sure that your categories are labeled “Absence” and “Presence,” not “0” and

“1.” Refer to Figure Pairs A-D as examples of what you should see.

Marker

● Marker options: Built-in, Filled in circles, Size = 10

Error bars → Standard deviation

● Direction: Both

● End Style: Cap

● Error amount: Custom → Select the cell in which you calculated the standard deviation in

Excel. You should select this cell for the positive and negative error values.

● Line: Solid line

● Color: Black

● Width: 1 pt

● Note: It is okay if the bars are not visible.

8. Based on the figure you made, describe how the absence or presence of GF-L affects the activity

of Receptor 1 (R1). (How does the activity of R1 in the absence of GF-L compare to the activity of

R1 in the presence of GF-L?)

Part 2 - Effect of GF-L on Activity of Receptor 2 (R2)

Directions: For questions 9-15, refer to the sheets titled “Q9-15 GF-L and R2.” This sheet contain the

activity (%) of Receptor 2 (R2) in the absence or presence of GF-L (sample size = 10 measurements per

category, absence or presence of GF-L). Create a column of dummy codes to represent the two

conditions, with 0 representing the absence of GF-L and 1 representing the presence of GF-L. Use Excel

for calculations, modeling, and graphing.

9. Calculate the slope of the linear relationship between the absence or presence of GF-L and the

activity of Receptor 2 (R2).

10. Calculate the intercept of the linear relationship between the absence or presence of GF-L and

the activity of Receptor 2 (R2).

11. Calculate the standard deviation of the linear relationship between the absence or presence of

GF-L and the activity of Receptor 2 (R2).

12. Calculate the mean activity of Receptor 2 (R2) in the absence of GF-L using μ = aX + b.

13. Calculate the mean activity of Receptor 2 (R2) in the presence of GF-L using μ = aX + b.

14. Use the sheet (tab) to create a plot of a linear relationship between the categorical independent

variable (absence or presence of GF-L) and the mean activity of Receptor 2 (R2). Your plot

should follow the formatting guidelines listed below.

Formatting Instructions

● Chart type: Line with Markers

● Quick layout: Layout 4

● Chart title: “Activity of R2 in response to GF-L”, Font size = 20

● Y-axis title: “Activity of R2 (%)”; Font size = 16

● Y-axis numbers: Font size = 14

● Y- axis minimum = 0, maximum =100

● X-axis title: “Absence or presence of GF-L”; Font size 16

● X-axis numbers: Font size = 14

● Line: No line

● Note: Make sure that your categories are labeled “Absence” and “Presence,” not “0” and

“1.” Refer to Figure Pairs A-D as examples of what you should see.

Marker

● Marker options: Built-in, Filled in circles, Size = 10

Error bars → Standard deviation

● Direction: Both

● End Style: Cap

● Error amount: Custom → Select the appropriate cell you calculated the standard

deviation you calculated the standard deviation for in Excel. You should select this cell for

the positive and negative error values.

● Line: Solid line

● Color: Black

● Width: 1 pt

● Note: It is okay if the bars are not visible

15. Based on the figure you made, describe how the absence or presence of GF-L affects the activity

of Receptor 2 (R2). (How does the activity of R2 in the absence of GF-L compare to the activity of

R2 in the presence of GF-L?)

Step 3: Weigh the evidence and conclude if GF-L binds to R1, R2,

both receptors, or neither receptor.

Because of your careful planning in Step 1 and your quantitative analyses in Step 2, you can now

conclude whether GF-L binds to R1, R2, both receptors, or neither receptor. Be sure to provide evidence

and reasoning that supports your claim.

16. The data supports the claim that____________. This conclusion is based on the observation that

____________.

Appendix 2

Which protein(s) in the cytoplasm are activated when a

receptor binds to Growth Factor L?

Now that we know which receptors bind Growth Factor L (GF-L), we can determine how this binding

affects the activity of proteins in the cytoplasm. Specifically, we are interested in the activity of five

proteins involved in the signaling pathway that regulates cell division: KR1, KR2, KR3, CDP1, and CDI2.

Figure 1 in Appendix 1 shows how these proteins are activated when the signal SR1 binds to Receptor 1.

To understand the cause of cancer in spotted gliders, we need to determine how GFL affects the state of

this signaling pathway by binding to Receptor 1 or Receptor 2.

The following steps are required to determine the effect of GF-L on the state of the signaling pathway:

Step 1: Determine whether the presence of GF-L affects the activity of each type of protein. This

step will help us determine which proteins are active in the presence of GF-L.

Step 2: Diagram the state of the signaling pathway in the presence of GF-L. Use your analysis from

Step 1 to conclude how GF-L affects the state of the signaling pathway that regulates cell division.

Step 1: Determine whether the presence of GF-L affects the

activity of each type of protein.

We performed an experiment in which GF-L was added to a tumor cell. From that experiment, I could

estimate each protein's activity in the presence or absence of GF-L. The proteins' activities are shown in

Figure 2 below.

Figure 2, long description

Figure 2. The relative activity of five proteins in the absence or presence of GF-L (Growth Factor L).

The top row of plots depicts the activities of KR1, KR2, and KR3 (left to right). The bottom row of plots

depicts the activities of CDP1 and CDI2 (left to right). Activity is measured from 0% to 100%. Filled

circles represent the mean activity, with error bars indicating standard deviation.

Using these data, you must conclude whether the presence of GF-L affects the activity of each type of

protein. Then, you can diagram the state of the signaling pathway in the presence of GF-L.

Directions: Use the data presented in Figure 2 to answer questions 17-21.

17. How does the presence of GF-L affect the activity of KR1?

a. KR1 is much less active in the presence of GF-L than in the absence of GF-L.

b. KR1 is much more active in the presence of GF-L than in the absence of GF-L.

c. KR1 has similarly low activities in the presence and absence of GF-L.

18. How does the presence of GF-L affect the activity of KR2?

a. KR2 is much less active in the presence of GF-L than in the absence of GF-L.

b. KR2 is much more active in the presence of GF-L than in the absence of GF-L.

c. KR2 has similar activities in the presence and absence of GF-L.

19. How does the presence of GF-L affect the activity of KR3?

a. KR3 is much less active in the presence of GF-L than in the absence of GF-L.

b. KR3 is much more active in the presence of GF-L than in the absence of GF-L.

c. KR3 has similar activities in the presence and absence of GF-L.

20. How does the presence of GF-L affect the activity of CDP1?

a. CDP1 is much less active in the presence of GF-L than in the absence of GF-L.

b. CDP1 is much more active in the presence of GF-L than in the absence of GF-L.

c. CDP1 has similar activities in the presence and absence of GF-L.

21. How does the presence of GF-L affect the activity of CDI2?

a. CDI2 is much less active in the presence of GF-L than in the absence of GF-L.

b. CDI2 is much more active in the presence of GF-L than in the absence of GF-L.

c. CDI2 has similar activities in the presence and absence of GF-L.

Step 2. Diagram the state of the signaling pathway in the

presence of GF-L.

Now that we have determined which proteins in the cytoplasm are active in GF-L presence, we are ready

to diagram the signaling pathway. The diagram will use symbols to illustrate which proteins are activated

or inactivated by a signal binding to the receptor.

A Fictional Example

Let's examine data for a fictional signaling pathway (Figure 3) consisting of a receptor, two secondary

messengers (SM1 and SM2), and two proteins that regulate cell activity (PRO1 and INH2). The

interactions between these proteins are already known, but the activation or inhibition of each protein

when a signal binds to the receptor is not provided. We must determine these effects and insert the

appropriate symbols to complete the pathway.

Figure 3 presents data on protein activity in the absence or presence of a signal. The top row shows the

activities of SM1 and SM2, while the bottom row shows the activities of PRO1 and INH2. SM2 and PRO1

exhibit low activity (5%) without a signal but increase to 90% when a signal is present, indicating

activation. Conversely, SM1 has low activity (5%) in the absence and presence of the signaling molecule,

and INH2 has high activity (90%) without a signal but drops to 5% in the presence of a signal, indicating

inhibition.

Figure 3, long description

Figure 3. The relative activity of four proteins (SM1, SM2, PRO1, and INH2) in the absence or

presence of a signaling molecule. The top row of plots shows the activities of SM1 (left) and SM2

(right). The bottom row shows the activities of PRO1 (left) and INH2 (right). Activity is represented as

a percentage from 0% to 100%.

Using this data, we can complete the pathway (Figure 4). A signaling molecule binds to the receptor,

activating SM1, which activates SM2 and PRO1. SM1 and SM2 undergo phosphorylation (represented by

a yellow phosphate symbol), and SM2 inhibits INH2 (represented by red perpendicular lines).

Take a moment to review the completed pathway and ensure it aligns with the data from Figure 4. Once

familiar with this example, you can analyze the signaling pathway in the cancerous cells of spotted gliders

using Figure 2 in Appendix 2.

Figure 4, long description

Signaling Pathway in Spotted Gliders

Figure 5 compares the healthy and cancerous signaling pathways. The left panel represents the healthy

pathway, where SR1 binds to R1, triggering the activation of proteins that promote cell division and

inhibiting proteins that suppress cell division. The middle panel is an incomplete cancerous pathway,

which includes both R1 and R2 receptors but lacks information on how proteins respond to GFL. The right

panel provides a key for activation, inhibition, and phosphorylation symbols.

Your task is to complete the cancerous pathway by determining how GFL affects the proteins in the

middle panel. Using Figure 2 data (Appendix 2, Step 1), consider:

● Which protein is directly activated or inhibited by R1 or R2 in the presence of GFL?

● How do the KR1, KR2, and KR3 data support your answer?

● How do the data for CDP1 and CDI2 support your answer?

22. Which protein is most likely to be directly activated by R1 or R2 when only GF-L is present?

a. KR1

Figure 4. A complete diagram of a fictional signaling pathway, illustrating protein activation,

inhibition, and phosphorylation. The signaling molecule binds to the membrane receptor,

which directly phosphorylates and activates SM2. SM2 then activates PRO1 while inhibiting

INH2, leading to increased cell division.

b. KR2

c. KR3

d. CDP1

e. CDI2

23. How do the KR1, KR2, and KR3 data support your answer?

24. How do the CDP1 and CDI2 data support your answer?

Directions: For question 25, use the CB Act 2 Workbook and refer to the sheet titled “Q25 Cancerous

Pathway.” Follow the five steps described below to complete the pathway when GF-L is present. To add

a symbol to the incomplete diagram, right-click on the symbol in the key and select "copy." Then, paste

this icon and drag it to the desired position in the incomplete diagram.

Figure 5, long description

Figure 5. Signaling pathways in a cancerous spotted glider. The left panel represents a key explaining

the components of the pathway. The right panel illustrates the cancerous signaling pathway, where the

signaling molecule GF-L binds to either the blue R1 receptor or the gold R2 receptor, activating a series

of secondary messengers (KR1, KR2, and KR3). This ultimately leads to increased activation of CDP1,

a protein that promotes rapid cell division, contributing to uncontrolled growth. CDI2, a protein that

normally inhibits cell division, remains inactive, further enhancing the cancerous process.

25. Follow the five steps below to complete the cancerous signaling pathway in the “Q25 Cancerous

Pathway” sheet of your CB Act 2 Workbook:

● Copy the orange GF-L symbol and place it at the active site of the appropriate receptor.

● Copy the yellow phosphorylation symbol and add it to all phosphorylated proteins

activated in the presence of GF-L.

● Copy the black activation arrows and place them between proteins that activate each

other in the presence of GF-L.

● Copy the red inhibition symbols and place them between the correct protein that

inhibits each other in the presence of GF-L.

● Copy the final activation arrow and add it to the correct locations where proteins

directly promote cell division in the presence of GF-L.

Appendix 3

Should we treat the cancer of spotted gliders with a drug or a

virus?

Thanks to your hard work, we now know how the presence of R2 and GF-L has disrupted the signaling

pathway that regulates cell division. This knowledge will enable us to evaluate potential cancer

treatments.

Your analyses indicated that the cancer results from an interaction between molecules of GF-L and

receptor(s) in the membranes of cells. Therefore, we might treat the cancer in either of two ways:

Treatment 1 - Antagonistic Peptide: A short chain of amino acids—a peptide—can inactivate a

signaling pathway by binding to the receptor and preventing a signal from binding. When designed as a

drug, such peptides bind more readily to the receptor than the signaling molecule; in this case, the drug

would be more likely to bind to the receptor than GF-L. This type of drug is called an antagonist or an

antagonistic peptide because the drug interferes with the function of the signaling molecule (called the

agonist). An antagonistic peptide that binds to the receptors for GF-L should prevent GF-L from

activating the signaling pathway that promotes cell division. Figure 6 illustrates the key differences

between a receptor agonist and a receptor antagonist.

Treatment 2 - Oncolytic Virus: A virus can enter a cell and use its machinery to reproduce, eventually

killing the cell in the process. A virus enters the cell by binding to a receptor on the surface of the

membrane. To bind to a receptor, the virus must have a protein on its surface that can bind to the

receptor; this protein is called a spike protein. Once inside a cell, the virus will replicate until the cell

bursts and dies. If a virus has a spike protein that binds to a receptor found solely in tumor cells, the virus

will kill tumor cells without affecting healthy cells. Such a virus is called an oncolytic virus, which means

"tumor-dissolving virus" in Latin. An oncolytic virus that binds to the receptors for GF-L should kill tumor

cells, without affecting healthy cells. Upon death, an infected tumor cell releases new viral particles that

spread to other tumor cells and potentially to other spotted gliders. Figure 6 illustrates the process by

which an oncolytic virus enters a cell and reproduces, eventually killing the cell.

Figure 6, long description

At the end of this assignment, you will recommend which of these two treatments the AI should use to

treat the spotted gliders. Table 3 provides a list of pros and cons for each treatment.

To design a treatment for the cancer in spotted gliders, you will need to follow these steps:

Step 1: Analyze Receptor 1 (R1) and Receptor 2 (R2) binding sites. This step will help us determine

the chemical properties of the receptors in tumor cells so we can determine the structure of an

antagonistic peptide or a spike protein that will bind to tumor cells but not to healthy cells.

Step 2: Identify the structure of a molecule that binds only to receptors in tumor cells. This step will

help us determine the structure of an antagonistic peptide or a spike protein that will bind to tumor cells

but not to healthy cells.

Step 3: Use a genetic code to design a sequence of RNA coding for a peptide or protein that binds

only to receptors in tumor cells. Use your analysis from Steps 1 and 2 to determine which nucleotides

are needed to code for amino acids that enable an antagonistic peptide or a spike protein to bind to tumor

cells but not healthy cells.

Step 4: Weigh the pros and cons of using a drug or a virus to treat the cancer of spotted gliders

and recommend a treatment. Recommend a treatment based on Steps 1-3, and explain why.

Figure 6. The left panel illustrates how receptor agonists and antagonists regulate cellular signaling.

Agonists activate receptors by binding and triggering a biological response, whereas antagonists

block receptor activation by preventing agonist binding. The right panel depicts the oncolytic virus

lifecycle, showing how a virus binds to a receptor, enters the cell, hijacks its machinery to replicate,

and ultimately causes lysis and cell death, releasing new viral particles.

Step 1: Analyze Receptor 1 (R1) and Receptor 2 (R2) binding

sites.

To design a treatment that targets tumor cells, we need to identify a molecule that can bind only to

receptors on the surface of tumor cells. Recall that R1 occurs on healthy and tumor cells, but R2

occurs only on tumor cells. Therefore, we need to identify a molecule that can bind to R2 but cannot

bind to R1. Fortunately, I could analyze the sequence of amino acids in each receptor type and model

the structure of its active site—the place where a signal would bind. Figure 7 shows the three amino acids

in each active site where the receptor must bind a signal.

Figure 7, long description

Binding between the receptor and the signal depends on the chemical properties of these amino acids.

Therefore, let's start by identifying these chemical properties. You may recall that life on Phygaris uses 21

amino acids, of which only 12 occur in life on Earth.

Directions: For questions 26-31, use CB Act 2 workbook and refer to the sheet titled “Q26-37 Amino

Acids Help.” Note that if an amino acid seems polar and contains a charge, focus more heavily on the

charge.

26. What is the chemical property of the R-group of alanosine?

a. nonpolar

b. polar

c. positively charged

d. negatively charged

27. What is the chemical property of the R-group of serine?

a. nonpolar

b. polar

c. positively charged

d. negatively charged

Figure 7. A peptide or spike protein must bind to each of the three amino acids that form the active site

of a receptor. The receptor R1 (left) contains the amino acids alanosine (Alo), serine (Ser), and

norvaline (Nor) at its binding sites. The receptor R2 (right) contains the amino acids mimosine (Mim),

valine (Val), and aminohexanedioic acid (Hex) at its binding sites. These differences in binding sites

determine the specificity of ligand-receptor interactions.

28. What is the chemical property of the R-group of norvaline?

a. nonpolar

b. polar

c. positively charged

d. negatively charged

29. What is the chemical property of the R-group of mimosine?

a. nonpolar

b. polar

c. positively charged

d. negatively charged

30. What is the chemical property of the R-group of valine?

a. nonpolar

b. polar

c. positively charged

d. negatively charged

31. What is the chemical property of the R-group of aminohexanedioic acid?

a. nonpolar

b. polar

c. positively charged

d. negatively charged

Step 2: Identify the structure of a molecule that binds only to

receptors in tumor cells.

Now that you have determined the chemical properties of the binding sites on each receptor, we can

design a molecule with chemical properties that promote binding to R2 but prevent binding to R1. Let’s

use oil, water, and magnets to better understand how amino acids interact and determine which

molecules will bind to R2 but not R1. Nonpolar amino acids behave like oil molecules—they don’t mix

with water and will only interact with other nonpolar amino acids through weak hydrophobic interactions.

Polar amino acids, on the other hand, are like water molecules—they readily form strong interactions

with other polar or charged molecules, just as water dissolves salt. Lastly, charged amino acids act like

magnets—positively charged amino acids attract negatively charged amino acids but repel other

positively charged amino acids, and vice versa. These principles will help guide your selection of amino

acids that bind to R2’s binding sites while avoiding interactions with R1.

To design a peptide that binds to R2 but not R1, you must first check the chemical property of each

binding site on R2. Then, select an amino acid that can bind to that site based on its polarity or charge,

making sure it cannot bind to the corresponding site on R1. When evaluating the answer choices,

compare the amino acids in the peptide to the binding site properties of both receptors. If an amino acid in

the peptide can interact with R2 but not R1, it is a correct choice. If it binds to both receptors (or neither),

it is incorrect.

Figure 8, long description

Let’s take glycine as an example to apply these concepts. Glycine is a nonpolar amino acid, meaning it

does not form strong interactions with polar or charged molecules. If an R2 binding site contains a

nonpolar amino acid, glycine could help establish a weak hydrophobic interaction with it. However, if the

corresponding site on R1 is polar or charged, glycine would not bind there, because nonpolar and polar

molecules do not interact well—just like oil and water. Now, let’s extend this logic to charged amino acids.

If R2 has a negatively charged binding site at position 1, while R1 has a nonpolar amino acid at the same

position, you would need to choose an amino acid with a positive charge because it would bind to R2’s

negative site but would not interact with R1’s nonpolar site. This pattern applies to all three binding sites

in Q32—your goal is to identify amino acids that form strong interactions with R2’s sites while avoiding

interactions with R1’s sites. By carefully selecting amino acids with the right polarity and charge, you can

design a peptide that binds selectively to R2 without binding to R1.

Directions: For questions 32-34, use the workbook and refer to the sheet titled “Q26-37 Amino Acids

Help.”

32. You need to design an antagonistic peptide (or spike protein) that binds to Receptor 2 (R2) but

does not bind to Receptor 1 (R1). Based on the chemical properties of the receptor binding

sites, which set of three amino acids should be used in the peptide to ensure it selectively binds

to R2 while avoiding R1?

a. Site 1: Val, Site 2: Gly, Site 3: Pyr

b. Site 1: Can, Site 2: Ile, Site 3: Val

c. Site 1: Ser, Site 2: Ile, Site 3: His

d. Site 1: Orn, Site 2: Val, Site 3: Mga

Figure 8. A table illustrating how amino acids bind to receptor sites based on their chemical properties.

Polar amino acids bind to polar binding sites, nonpolar amino acids bind to nonpolar binding sites, and

charged amino acids bind to oppositely charged binding sites. The reasoning column explains why

these interactions occur, using analogies to water, oil, and magnets to help students understand

molecular interactions.

e. Site 1: Tyr, Site 2: Orn, Site 3: Pyr

33. Based on your answer to Question 32, why do the three selected amino acids in the antagonistic

peptide successfully bind to Receptor 2 (R2)?

34. Based on your answer to Question 32, why do the three selected amino acids in the antagonistic

peptide fail to bind to Receptor 1 (R1)?

Step 3: Use a genetic code to design a sequence of DNA

coding for a peptide or protein that binds only to receptors in

tumor cells.

Thanks to your careful analysis, we know which amino acids are needed to create a peptide or protein

that binds to R2 but not R1. We can use this information to synthesize many molecules targeting the

tumor cells in spotted gliders.

If we use an antagonistic peptide or an oncolytic virus to treat cancer, we must synthesize these

molecules in the lab by using DNA to code for the necessary amino acid sequences. Proteins are

artificially produced by transcribing DNA into mRNA and translating mRNA into amino acids, but

selecting the correct DNA sequence is crucial to ensure the treatment targets only the tumor receptors

(R2) and not normal cells (R1).

To determine the correct DNA sequence, we must use the genetic code of Phygaris, which differs from

Earth's genetic code. While Earth's DNA consists of adenine (A), thymine (T), cytosine (C), and

guanine (G), Phygaris DNA uses cytosine (C), guanine (G), xorine (X), and yolocine (Y) as its four

nucleotides. Figure 9 compares Earth’s DNA with Phygaris DNA, showing their structural similarities and

differences.

Figure 9, long description

Figure 9. A side-by-side comparison of the molecular structure of DNA on Earth versus Phygaris. Both

structures have a double helix structure, with complementary strands of DNA running antiparallel to one

another (5’ to 3’ on one end and 3’ to 5’ on the complementary strand). Both versions of DNA have a

sugar-phosphate backbone with nucleotides hydrogen bonded in the middle of the double helix

structure. Both structures have complementary base pairing between two pairs of nucleotides. In DNA

found in organisms living on Earth, the nucleotide base pairs are (1) guanine (G) and cytosine (C) and

(2) adenine (A) and thymine (T). In DNA found in organisms living on Phygaris, the nucleotide base

pairs are (1) guanine (G) and cytosine (C) and (2) xorine (X) and yolocine (Y).

On Phygaris, proteins are encoded by codons, which are sequences of three nucleotides that specify

particular amino acids. The genetic code of Phygaris contains 64 codons, 61 of which correspond to the

21 amino acids used by spotted gliders. For example, the codon YCX codes for threonine, while GCX

codes for norvaline. Figure 10 shows how to read the codon chart:

Figure 10, long description

Figure 10. The genetic code of Phygaris consists of 64 codons representing 21 amino acids.

● The first base is found in the leftmost column.

● The second base is in the top row.

● The third base is in the rightmost column.

● The intersection of these positions determines the amino acid.

To practice, let’s consider the amino acid proline. According to the genetic code, proline is encoded by

CCX, CCC, CCY, and CCG (highlighted in Figure 11). Once you understand this example, you can

identify the correct codons needed to synthesize a peptide that binds to R2 but not R1.

Figure 11, long description

Figure 11. Four codons represent proline in the genetic code of Phygaris: CCX, CCC, CCY, and CCG.

These codons are highlighted in the red box.

Use Table 1 to help you simplify your task. First, enter the three amino acids needed for a molecule to

bind to the receptors of tumor cells; these amino acids are listed in your answer to Question 32. Then,

enter all codons in the genetic code of Phygaris that correspond to each of the three amino acids.

Directions: For questions 35-37, use the workbook and refer to the sheet titled “Q26-37 Amino Acids

Help.” You can use Table 1 above to fill in the correct amino acids and their respective codons. This table

is also found on tab “Q26-37 Amino Acids Help” if this is more convenient for you.

35. Which codons of DNA correspond to the amino acid at the first binding site of the antagonistic

peptide/spike protein needed to bind to the receptors of tumor cells? Check all that apply.

a. XXX

b. XCX

c. XYY

d. XXC

e. XCC

f. XCG

g. XCY

h. YCY

36. Which codons of DNA correspond to the amino acid at the second binding site of the

antagonistic peptide/spike protein needed to bind to the receptors of tumor cells? Check all that

apply.

a. XXY

b. YXX

c. YXC

d. CXY

e. YXY

f. GXC

g. GXY

h. YXG

37. Which codons of DNA correspond to the amino acid at the third binding site of the antagonistic

peptide/spike protein needed to bind to the receptors of tumor cells? Check all that apply.

a. GYY

b. YYY

c. YCC

d. YGC

e. CYX

f. CCX

g. XCY

h. CYC

Table 1. Amino acids at binding sites 1, 2, and 3 of the antagonistic peptide/spike protein are needed to bind to the

receptors of tumor cells and the amino acids' corresponding codons.

Binding site Amino Acid Codons

1

2

3

Step 4: Weigh the pros and cons of using an antagonistic

peptide or an oncolytic virus to treat the cancer of spotted

gliders.

Now that we can design a peptide or protein targeting tumor cells, we must decide which treatment to

deliver to spotted gliders.

Should we design an antagonistic peptide that binds to Receptor 2? Or should we design a spike

protein that enables a virus to bind to Receptor 2, ultimately allowing the virus to enter the cell,

replicate new viral particles, and kill the cell?

Because each treatment has pros and cons, you should carefully weigh the pros and cons in Table 2

before recommending one. I will consider your argument when deciding how to treat the cancer of the

spotted gliders.

Table 2. Pros and cons associated with each of the two treatments: an antagonistic peptide or an oncolytic

virus.

Treatment Pros Cons

Antagonistic peptide Inhibits cell division by binding

directly to R2, making it less likely

to fail because of interactions with

proteins inside the cell.

Must be delivered to each

organism, which means each

organism must be captured and

treated to save a population.

Less likely to induce an immune

response than a virus, reducing

side effects such as fatigue,

nausea, and pain.

Will not kill the cell; therefore,

normal signals such as SR1 could

still cause a tumor cell to divide.

Oncolytic virus Kills tumor cells, preventing the

spread of the cancer within and

between gliders.

Must enter the cell and reproduce

to kill the cell; therefore, the virus

could fail to reproduce inside the

cell.

Spreads from glider to glider,

which means one may need to

treat only a few gliders to save

the population.

Can be deactivated by the

immune system before killing the

tumor cells.

Attract immune cells to the region

of the body where the tumor cells

occur, which could enable these

immune cells to detect and

destroy tumor cells.

Can induce side effects, including

fatigue, nausea, and pain, which

could limit an organism's ability to

evade predators and find food.

Directions: Use the information in Table 2 and your understanding of receptors in tumor cells to answer

Question 38.

38. Fill in each blank with Antagonistic peptide or Oncolytic virus:

The ___________ kills tumor cells directly and can spread from one glider to another, potentially reducing

disease transmission. In contrast, the ___________ must be delivered to each organism individually,

which makes treating an entire population more labor-intensive. The ___________ is less likely to cause

severe side effects, such as fatigue, nausea, or pain. However, the ___________ can be cleared by the

immune system before it reaches all the tumor cells. Overall, the benefits of the ___________ outweigh

those of the other treatment because it can definitively kill cancerous cells, while the other treatment