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DISCUSSION ACTIVITY WEEK 3

Group Members _________________________ _________________________

Manager Recorder

_________________________ _________________________
Spokesperson Reflector

THE PLAN: Our big overarching goal is to figure out how enzymes work in extreme environments. Last
week, we talked about how enzymes can impact reactions in the body by acting as a catalyst. Today we are
going to look further at how enzymes work. In this case, we are not going to look at just the active site but
expand this to look at protein folding and how that relates to entropy.

The learning objectives and skills for today’s session are for you to:

Learning Objective Skill

Predict whether a reaction is energetically favored List factors that determine energetic stability
based on the relative strength of chemical bonds
and intermolecular forces in reactants and products
Predict whether a reaction is entropically favored List factors that determine the number of
based on the state of matter, molar mass, and configurations for the system (matter and energy)
complexity of reactants and products Explain how/why factors affect entropy values
Compare systems in terms of the relative number
of distinguishable configurations
Qualitatively predict the effect of changing List factors that determine overall thermodynamic
temperature on reaction directionality based on the stability
relative energetic stability of reactants and products

As explained in week 1, each member of the team will be assigned to a specific role, which will rotate each
week. The recorder should note who is performing each role in a given week. It is the responsibility of
all group members to double check that they are tagged on the Gradescope group submission and
that all pages of the correct document were uploaded to Gradescope before the deadline.

Recorder: Records answers for the team and submits the team report on Gradescope.

Reflector: Reads the questions and checks that the final conclusion makes sense and ensures that
all members have consistent answers.

Spokesperson: Presents answers (or questions) to the class, instructor, or other teams.

Manager: Keeps the team on task and on schedule. Considers how the team is working and how it
could improve in the future.

THE STABILITY OF PROTEIN FOLDING

Watch the following video that discusses protein folding

(https://www.youtube.com/watch?v=hok2hyED9go) before you come to class. Take the first few minutes
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to talk about the major points of the video as a group and then work together to answer the questions
below. The recorder of the group should write down the responses to these questions and submit to
Gradescope after class – make sure to record the names of team members present at the top of the page
and select those team members when you submit the assignment.

1. Briefly summarize what you learned about different levels of protein folding from the video.

2. a. Sketch a simple picture of both a folded and an unfolded protein. This can be represented as just
a line.

b. Thinking about your answer to question number 2a, which configuration do you expect to be
preferred? Justify your answer.
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3. Energetic factors focus on the potential energy of the substance due to interactions between
submicroscopic components (i.e., electrons, atoms, ions, molecules). For protein folding, this is
related to the intermolecular forces. What type or types of intermolecular forces are involved in
protein folding?
(HINT: This was discussed in Principles I and can be found in pages 195-196 of your textbook.)

4. Stronger interactions lead to a more thermodynamically stable state (energetically favored).

Looking at the corresponding image, which of the interactions that you have listed in question 3
do you think protein folding maximizes to lead to the most thermodynamically stable state?
Justify your answer.

5. Protein folding is largely influenced by the interaction of the R-groups (side chains) with the
environment. Explain how this interaction relates to the polarity of the R-groups. How does the
fact that the proteins must fold in certain ways because of these interactions affect the number of
configurations available to the protein?
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6. We also have to think about entropic factors when we think about thermodynamic stability.
Entropic factors influence the number of different configurations in which submicroscopic
components of the substance may exist. Think about your answer to question 5 – Does protein
folding increase or decrease entropy? Justify your answer.

7. Consider the role of energetic and entropic factors for protein folding.
a. Draw a PEC diagram that represents the relative potential energy and number of
configurations for the unfolded and folded protein.

b. Explain which factor(s) provide the driving force(s) for protein folding.

REFLECTING ON SKILLS

An important part of developing skills that are important for supporting your learning (and that are highly
valued by employers) is to assess your progress and identify areas where you can improve.
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Critical Forming an argument or reaching a conclusion supported with evidence and

Thinking reasoning by evaluating, analyzing, and/or synthesizing relevant information.

Category Ratings Observable Characteristics

Stated the conclusion or the
Made an argument that includes a claim (or position),
claim of the argument
supporting information, and reasoning
Listed the evidence used to
support the argument
Linked the conclusion/claim
0 1 2 3 4 5 to the evidence with focused
and organized reasoning
No Incomplete Partial Complete State any qualifiers that limit
evidence the conditions for which the
argument is true
Forming Suggestions for Improvement:
Arguments a) Review the original goal—what question were you trying to answer?
(Structure) b) Clearly state your answer to the question (your claim or conclusion).
c) Review the information you previously evaluated, analyzed, and/or synthesized, and
decide what evidence supports your claim.
d) State/summarize the evidence clearly, including: what samples are being studied, how
the results from the samples compare with one another (e.g. “faster than”, “smaller
than”), relevant statistical information (e.g. mean, standard deviation, statistical test
used, and p-value), and how much difference was measured (e.g. “10% faster”, “three
times larger”)
e) Explain how each piece of information links to and supports your answer.
f) Make sure the claim, supporting information/data, and reasoning are all present in your
answer, and that the claim/conclusion answers the question.
g) List the conditions for which the claim holds true or is no longer valid

Indicate the number on the rubric you think best characterizes your level of acting as a cohesive unit today.
Why did you give your team this rating? Provide specific evidence related to your interactions an observer
would have seen to support this rating.

What is one way you can improve your performance next week? How do you plan to achieve this?
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CONTINUING ON ...

8. Open the simulation on protein folding found on page 201of your textbook
https://lab.concord.org/embeddable.html#interactives/samples/5-amino-acids.json
Notice that you can change both the solvent type and the hydrophobicity of the protein. Change the
settings to “all hydrophobic.”
a. Before running the simulation, predict what you think will happen to the protein if you set the
solvent to water and provide a justification.

b. Run the simulation to see if you were correct. Was your initial prediction correct?

9. Now change the simulation settings to water and mostly hydrophilic amino acids.
a. How does this change the protein folding process?

b. Provide a hypothesis to explain this observation.

10. Looking at the simulation, how do you think that the hydrophobicity/hydrophilicity of the amino acids
in an aqueous solution impacts the entropic factors?