Tag: Model Answer

Assignment Prompt & Instructions

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
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