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Link to my evolving "pacing guide" with hyperlinks to activities, etc.

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Link to my evolving "pacing guide" with hyperlinks to activities, etc.

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Jackson Labs - Teaching the Genome Generation

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Jackson Labs - Teaching the Genome Generation

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Teaching the Genome Generation - New England

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Teaching the Genome Generation is a one-week professional development short course in genomics, bioinformatics, and ethics for high school science teachers, funded by the NIH Science Education Partnership Award (SEPA) program.

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Group 6

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Group 5

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Group 4

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Group  3

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#3 EVOLUTION PROJECT Essential knowledge 1.A.4

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Group 2

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evol project rubric

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Group 1

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Evolution Project

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wooly worm chi squaretable with other math stuff

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We will be using Allele a1 here

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AlleleA1 simulates evolution at a single locus in an ideal population of imaginary organisms. The locus of interest has 2 alleles: A1 and A2. The user enters values for parameters controlling selection, mutation, migration, genetic drift, and inbreeding. As the simulation runs, the software plots a graph showing the frequency of allele A1 over time.

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Explore Biology | AP Biology Teaching & Learning Resources

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Graham Walker, Monitoring Editor

Abstract

This article describes a simple and inexpensive hands-on simulation of protein folding suitable for use in large lecture classes. This activity uses a minimum of parts, tools, and skill to simulate some of the fundamental principles of protein folding. The major concepts targeted are that proteins begin as linear polypeptides and fold to three-dimensional structures, noncovalent interactions drive this folding process, and the final folded shape of a protein depends on its amino acid sequence. At the start of the activity, students are given pieces of insulated wire from which they each construct and fold their own polypeptide. This activity was evaluated in three ways. A random sample of student-generated polypeptides collected after the activity shows that most students were able to create an appropriate structure. After this activity, students (n = 154) completed an open-ended survey. Their responses showed that more than three-quarters of the students learned one or more of the core concepts being demonstrated. Finally, a follow-up survey was conducted seven weeks after the activity; responses to this survey (n = 63) showed that a similar fraction of students still retained these key concepts. This activity should be useful in large introductory-level college biology or biochemistry lectures.

INTRODUCTION

Gaining an understanding of the fundamental principles of protein folding is an important part of most introductory-level undergraduate biology and biochemistry courses. At the introductory level, an appropriate understanding of protein folding would include the following three major concepts:

1. A protein is synthesized as a linear chain of amino acids that then folds into a complex three-dimensional shape.

2. Noncovalent interactions (hydrogen bonds, electrostatic interactions, van der Waals bonds, and hydrophobic interactions) as well as covalent interactions (e.g., disulfide bonds) between different parts of the protein chain drive the folding process.

3. The final folded shape of the protein depends on its amino acid sequence.

Because these concepts involve complex three-dimensional molecules, two-dimensional blackboard and textbook presentations often do not communicate them effectively. Many instructors therefore use supplemental methods, including molecular visualization, and, in some cases, hands-on demonstrations and activities. Molecular visualization (MolVis) software allows the user to achieve a three-dimensional impression by manipulating a two-dimensional image of a particular molecule. There are a large variety of MolVis programs, sites, and tutorials available to educators (e.g., Martz, 2001 Khoo and Koh, 1998 White et al., 2002 Roberts et al., 2005 ). ; ; ); these tools have been shown to be effective for teaching purposes (

As an example of protein folding, I have used molecular visualization presentation of hemoglobin in my lectures for several years ( White et al., 2002 ). During this presentation, I would explain how the protein began as a linear chain and then folded, citing key noncovalent interactions that give the protein its final folded shape. Although I have been pleased with the results, I wanted to find a hands-on physical model that would show how the folding process proceeds rather than working backward from a fully folded protein. I wanted each of the roughly 200 students in lecture to simulate the folding of their own protein so as to get a visual and tactile "feel" for the process. I wanted this activity to show how a linear chain of amino acids can fold into a three-dimensional shape based on interactions between parts of the chain even if the activity did not simulate all of the factors involved in this process. Furthermore, I wanted this activity to fit within the spatial, temporal, and logistic constraints of a 50-min lecture in a typical large lecture hall. Consequently, the activity needed to be inexpensive, require a small number of parts, and require no special tools or accessories.

Research on the efficacy of hands-on modeling of chemical and biological structures has shown encouraging results. There have been several studies ( Howe and Durr, 1982 Copolo and Hounshell, 1995 Barnea and Dori, 1999 Gabel and Sherwood (1980) Roberts et al. (2005) showed that physical models combined with MolVis helped students to learn about protein structure. In their study, students reported that hands-on modeling using rigid models of fully folded proteins was the most helpful mode for teaching these concepts. These results, combined with my experience teaching this material, suggested that using a hands-on activity in lecture would likely be productive. showed that a year-long, model-based chemistry curriculum had improved learning outcomes compared with traditional instruction. ) where use of physical models of simple chemical structures, combined with other innovations, showed increased learning compared with traditional curricula. ; ;

Several hands-on protein folding activities have been developed by others. Martz (2005) recommends using Toobers-long wires wrapped in foam rubber-to simulate protein folding. Others have developed a set of highly realistic activities using Toobers with attached magnetic side chains ( Nelson and Goetze (2004 ) developed an elegant demonstration of protein folding that uses pipe cleaners to simulate the protein chain. However, distributing and assembling the several pipe cleaners, tape, and binder clips required for this activity would not be easy or rapid on the small desks found in most large lecture halls. www.moleculardesigns.com/toobers.php). Unfortunately, although Toobers are relatively inexpensive, it is still prohibitively costly to give each of the 200+ students in lecture a Toober kit of their own.

Given these constraints, I have developed a simple simulation that uses a single piece of wire to simulate a small polypeptide chain. This activity illustrates the three core concepts of protein folding described and can be easily carried out by students in a large lecture class. I have conducted a preliminary evaluation of the activity that shows that it is effective in conveying these concepts.

INSTRUCTIONAL CONTEXT

I use this activity in General Biology I (Bio 111) at University of Massachusetts (Boston, MA). Bio 111 is the first course of a two-semester introductory biology series for biology majors. Bio 111 covers genetics, biochemistry, cell biology, and molecular biology. The course consists of a 50-min lecture three times a week and 10 laboratory sections that meet once a week for 3 h. I give the lectures and supervise the graduate teaching assistants who teach the laboratories.

There are roughly 240 students enrolled in the class in any given semester. The students in Bio 111 are a rather diverse group compared with many introductory-level science courses; about 75% are female, 40% are nonwhite, and their average age is 22 yr. Roughly one-third (29%) are majors in biology-related subjects (biology, biochemistry, premedical), and a similar fraction (35%) are undecided as to their major. For many of these students, 48% of whom are freshmen, this course is their first college science course and their first science course in several years.

I am able to determine the number of students attending each lecture by using the Personal Response System ( www.gtcocalcomp.com/interwriteprs.htm), where each student answers multiple-choice questions in lecture by using an individual infrared transmitter. On the day that I conducted the first phase of the evaluation of this activity, there were 189 students in the lecture hall.

I use this activity during my first lecture on protein structure. Before this lecture, I have introduced basic chemistry as it applies to proteins (covalent and noncovalent bonds) and the idea of polymers. I begin this lecture by talking about amino acid structure-backbone and side chain-and then describe how amino acids are linked to form protein chains. I then discuss, with examples, the different properties of amino acid side chains. Finally, I show them the three-dimensional shape of hemoglobin by using molecular visualization software and explain that proteins have complex three-dimensional folded shapes. This sets up the background for the activity.

LECTURE ACTIVITY

For the activity, each student is provided with a 4-ft length of 18-gauge insulated wire. This wire is available from many sources. 1 In addition, each student receives a handout that explains how to use the wire to simulate a polypeptide chain. This handout can be accessed online in .pdf and .doc format at http://intro.bio.umb.edu/BW/WireDemo.html. These instructions, combined with guidance from the lecturer, are sufficient for the students to perform the activity during the lecture.

First, I explain how their wire will model a short polypeptide chain (as shown in ). The straight part of the wire simulates the backbone, and the loops simulate the side chains. Large open loops (large enough to accommodate two fingers) represent hydrophobic side chains, long closed loops (four twists) represent positively charged side chains, and short closed loops (two twists) represent negatively charged side chains ().

Students are then told to twist their wire to make their own six- to eight-amino acid polypeptide chain. They twist the wire to form loops corresponding to their choices of hydrophobic, anionic, or cationic side chains, leaving three finger-widths of space between each side chain. The simulation works better if they make more hydrophobic side chains than charged side chains and if they also make at least one anionic and one cationic side chain. It takes students ∼3-4 min to twist their wires to produce their linear polypeptides.

At this point, I tell the students that they have just made a simulated short polypeptide. I ask them what they would expect the hydrophobic side chains to do when surrounded by water. Based on our discussions of the hydrophobic effect, they predict that the hydrophobic side chains would cluster in the center of the protein. I tell them to do this with their wires; they then fold their wires into compact three-dimensional structures with the hydrophobic side chains inside. I then ask them what the anionic and cationic side chains would do. When they respond with "form ionic bonds," I tell them to do this with their models as well; they bring the anions to the cations as much as possible while keeping the hydrophobic side chains inside.

At this point, they each have a little ball of wire simulating their fully folded protein. I then ask them the following questions and discuss the answers (in parentheses):

1. What holds your polypeptide in its shape? (Ionic bonds and hydrophobic interactions.)

2. Why is the shape of your polypeptide different from that of your neighbor? (They have different amino acid sequences.)

Finally, I have them simulate thermal denaturation by having them hold their proteins by one part of the backbone and shake them to simulate heating. I explain that this would break the weakest bonds first; that is, the noncovalent bonds. As a result, the proteins then become denatured-they lose their proper folded shape. I explain that this often exposes their hydrophobic side chains to the solvent. The hydrophobic side chains from different molecules can then aggregate-molecules held by neighboring students can link together. I explain that this is what happens when, among other things, egg whites are cooked. We then move on to a molecular visualization-based presentation on an actual protein, hemoglobin. From start to finish, the activity takes roughly 10-12 min.

EVALUATION

The first part of the evaluation was designed to assess the degree to which they understood and followed the directions. I collected a sample of 24 folded wires after the lecture. The majority (19 or 79%) had between six and eight amino acids. Twelve of the 24 "polypeptides" (50%) made by the students had a mixture of hydrophobic, cationic, and anionic side chains; another eight (33%) had hydrophobic and either cationic or anionic side chains. Only four of the 24 (17%) polypeptides had only hydrophobic side chains or were uninterpretable. Overall, 79% had an acceptable structure: six to eight side chains and a mixture of hydrophobic and charged side chains. Several wires from this sample are shown in . The best of these (a) clearly shows the different side chain types; others (, b-d) show some of the mistakes that students made. These mistakes include having more hydrophilic than hydrophobic side chains (b), having only hydrophobic and cationic side chains (c), and not twisting the wire properly (d).

The second part of the evaluation assessed their learning of the three major concepts by using a short anonymous voluntary survey conducted in lecture immediately after the activity. A voluntary survey was chosen for its simplicity of administration; furthermore, response rates to previous voluntary surveys have been high. There were two forms of the survey distributed randomly to the class. These two different surveys were used to approach the students' learning from different perspectives and thereby yield a richer set of responses. Roughly one-half of the students received survey A, which asked the following:

1. What did you learn about proteins from the wire demonstration?

2. What about proteins was still unclear after the wire demonstration was finished?

3. How could the wire demonstration be improved?

The other one-half of the students received survey B, which asked the following:

1. Give one feature of the wire demonstration that accurately simulates the way proteins fold and explain why it is realistic.

2. Give a feature of the wire demonstration that does not accurately simulate the way proteins fold and explain why it is unrealistic.

3. How could the wire demonstration be improved?

There were 82 responses to survey A and 72 responses to survey B. The total of 154 surveys represents 81% of the 189 students in lecture. These responses were then scored based on the three major concepts described previously.

When asked what they had learned from the demonstration (survey A, question 1), 63 responses (77%) mentioned at least one of the major concepts. When asked what was still unclear (survey A, question 2), only 11 (13%) of the responses listed any of the major learning goals. Similarly, 59 (82%) of the responses reported that at least one of the major concepts was represented accurately by the activity (survey B, question 1) and only 11 (15%) of the responses indicated that one of these was not represented accurately by the activity (survey B, question 2).

These results can be further analyzed by the specific type of response, as shown in and . shows the eight most frequent response classes to the questions that asked for what the students learned or what was represented accurately (survey A and B, question 1). The three major concepts are the most frequently given responses. Students' responses also show several other notable learning outcomes including a "feel" for the process and an understanding of the difference between backbone and side chains. shows the eight most frequent response classes to the questions that asked for what was still unclear or not accurately represented by the activity (survey A and B, question 2). Only one of the three learning goals (Concept [2]) is represented in these responses and was only mentioned by three students (4%). The most frequent category of response was that the exercise was fine as it is. These responses also reveal some physical difficulties with the wire and suggest that taking more time with the activity would be productive.

Table 1.

What did you learn about proteins from the wire demonstration? (n = 82)

Give one feature of the wire demonstration that accurately simulates the way proteins fold and explain why it is realistic. (n = 72)

1. 35 (43%) Hydrophobic/hydrophilic interactions. Concept (2).

1. 45 (62%) Hydrophobic/hydrophilic interactions. Concept (2).

2. 32 (39%) Protein folding process. Concept (1).

2. 20 (28%) Protein folding process. Concept (1).

3. 19 (23%) Ionic interactions. Concept (2).

3. 11 (15%) Ionic interactions. Concept (2).

4. 11 (13%) Sequence determines structure. Concept (3).

4. 5 (7%) Backbone versus side chain.

5. 11 (13%) Denaturation.

5. 5 (7%) A tactile or visual ′feel′ for what was going on.

6. 10 (12%) Vague mention of ′proteins′ only.

6. 4 (6%) A protein as a three-dimensional object.

7. 8 (10%) A tactile or visual ′feel′ for what was going on.

7. 3 (4%) Denaturation.

8. 7 (8%) Miscellaneous.

8. 3 (4%) Vague mention of ′proteins′ only.

Table 2.

What about proteins was still unclear after the wire demonstration was finished? (n = 82)

Give a feature of the wire demonstration that does not accurately simulate the way proteins fold and explain why it is unrealistic. (n = 72)

1. 50 (61%) ′Nothing,′ blank, ′all clear.′

Biological issues

2. 14 (17%) Questions beyond the scope of the demonstration.

1. 20 (28%) ′Nothing,′ blank, ′fine,′ etc.

3. 4 (5%) Denaturation.

2. 12 (17%) ′In real life, a protein only folds one way.′

4. 3 (4%) ′How the amino acids are joined by the backbone.′

3. 6 (8%) ′Wire does not show how interactions work.′

5. 3 (4%) Ionic or hydrophobic/hydrophilic interactions. Concept (2).

4. 6 (8%) Issues beyond the scope of the demonstration.

6. 2 (2%) ′I'm not sure-I'm just a little fuzzy.′

5. 5 (7%) ′Real proteins have more amino acids.′

7. 2 (2%) Backbone versus side chain.

6. 4 (6%) ′Folding wire is not like real folding.′

8. 2 (2%) Uninterpretable.

7. 4 (6%) ′It's wire.′

8. 3 (4%) ′Wire does not show structure completely.′

Physical/logistical issues

1. 4 (6%) ′Hard to fold the wire.′

2. 3 (4%) ′Wire too floppy.′

3. 2 (3%) ′Took too short a time.′

Finally, both versions of the survey asked how the activity could be improved. Responses to this question from all 154 surveys were pooled to give Box 1. The majority (52%) of the responses said that the activity was fine as it is. The remainder suggested various improvements to the activity some of which we will adopt in future lectures (clearer instructions and taking more time to explain the activity).

Box 1. Survey responses: suggested improvements:

Improvements (pooled from both surveys; n = 154)

1. 81 (52%) "None," blank, "fine as it is."

2. 13 (8%) "Use more flexible wire."

3. 8 (5%) "Color wire by amino acid properties."

4. 7 (4%) "Spend more time on the demonstration."

5. 5 (3%) "Give clearer twisting instructions."

6. 5 (3%) "Give clearer folding instructions."

7. 4 (2%) "Allow neighbors to attach wires together."

8. 3 (2%) "Explain denaturation more."

The third part of the evaluation measured the longer-term effects of this activity using a follow-up survey conducted at the end of the semester, approximately 7 wk after the activity. This survey was based on survey A, question 1, which asked what students had learned from the activity. To avoid excessive prompting, the follow-up survey questions, shown below, do not mention proteins.

Consider the lecture demonstration from the biochemistry section of the class where you each twisted up a piece of blue wire. As a reminder, the wire is shown below (at greatly reduced scale). (The survey included a reduced version of that only showed the wire; none of the lines or text was included.)

1. Do you remember this demonstration? (circle one) Yes No

2. If you answered "Yes" to (1i), please describe what you remember learning from this demonstration. If "No", go on to (2).

There were 144 students in lecture on the day when I carried out this follow-up evaluation. Of these 144 students, 63 (44%) handed in responses to this voluntary survey. Of the 63 students who responded, 61 (97%) stated that they remembered the activity. Of the 63 responses, 53 (84%) included one or more of the major concepts. A summary of the eight most common responses is shown in Box 2. These data show that Concepts (1) and (2) were represented in a large fraction of the responses. In addition, this survey reveals two new response categories. The first, "Side chain interactions determine structure" is closely related to Concept (3). The second, "Different-shaped loops represent different types of side chains," shows that these students remembered some of the details of the activity.

Box 2. Follow-up survey responses: positive outcomes (n = 63)

1. 35 Hydrophobic/hydrophilic interactions. Concept (2).

2. 29 Protein folding process. Concept (1).

3. 8 Side chain interactions determine structure.

4. 7 Different-shaped loops represent different types of side chains.

5. 6 Ionic interactions. Concept (2).

6. 2 Backbone versus side chain.

DISCUSSION

The results show that this is a highly successful activity. Students were, in general, able to twist the wire as instructed. Immediately after the activity, students listed the three major concepts as having been learned or represented accurately in the majority of their responses; these concepts were mentioned by only a small minority as being unclear or inaccurately represented. The fraction of students mentioning at least one major concept (75-80%) is very high, given the brevity of the activity. Although self-reported measures are not as reliable indicators of learning as formal content-based pre- and postactivity surveys, our design avoids some of the weaknesses of this type of analysis. Because we used open-ended questions where the students had to name the concepts without prompting, this analysis is less susceptible to novelty, "leading the witness," and "pleasing the teacher" effects than if we had used multiple-choice content questions or measures of attitude or satisfaction.

The follow-up study shows that students retained several of the learning goals of the activity for at least 7 wk. However, because of the low response rate, the percentage of students remembering the three major concepts should be viewed as an overestimate of retention, because it is likely that students who remembered the activity would be more likely to return the survey form. Even given these reservations, it is clear that this activity had a lasting impact on the students.

In addition to the effects documented above, this activity has other valuable outcomes. It shows students how proteins fold themselves and that this type of self-assembly is possible: although proteins have complex three-dimensional shapes, they are not stamped out of a mold. It provides a concrete illustration of the protein folding process, rather than the endpoint shown by textbook diagrams and molecular visualization. Finally, the demonstration provides a valuable referent for later lectures. As the course progresses, I am able to refer to the wire demonstration as a concrete example when talking about backbone-side chain issues, folding of other proteins, and side chain interactions.

Although there are many positive outcomes from this activity, it should be noted that this highly simplified model of protein folding can lead to important misconceptions, which may need to be specifically addressed with the students. These misconceptions arise from five features of the activity-simplifications inherent in the wire model of protein structure that have important consequences. First, when students twist the side chains along the length of the wire, this implies that the amino acids are formed out of the same material as the backbone rather than being assembled in order from premade monomers. In addition, it implies that hydrophobic side chains are always larger than charged side chains. Second, the activity does not simulate hydrogen bonds; it would be hard to make five distinguishable kinds of loops, and, with only seven amino acids in the chain, it would be difficult to simulate three different types of interactions. Similarly, the activity does not include the effects of side chain shape or covalent bonds between side chains. Third, it suggests that the formation of a hydrophobic core is always the first step in protein folding. Fourth, because the backbone is "inert" in the activity and the polypeptides are short, it is not possible to demonstrate secondary structure. Moreover, these short polypeptides are also incapable of adopting the range of complex three-dimensional shapes formed by full-length proteins. Finally, the wire does not illustrate the amino and carboxy ends of the protein or the directionality of the backbone. Depending on the level of understanding desired by individual instructors, it will be important to discuss some or all of these issues in the context of further treatment of protein folding. This discussion also could lead to a productive conversation about the role of models in science as well as the illustrative and misleading features of any model. Bearing in mind that this activity is designed as an illustration and to provide a referent for later elaboration, rather than as a complete exposition, it is an effective introduction to protein structure and folding.

Footnotes

¹ Insulated 18-gauge copper wire is available at most hardware stores. I recommend 18-gauge because thinner gauges are too flexible to hold the final folded shape of the protein, and thicker gauges are too stiff to twist into amino acid side chains. Precut 4-ft lengths of this wire (part no. 9504) are available from Advanced Wire and Cable (Xenia, OH) ( www.advancedwire.com) at a cost of $0.30 each (minimum order $50.00). Shorter wires do not allow a sufficient number of amino acids; longer wires are cumbersome and hazardous in a crowded lecture hall.

REFERENCES

Martz E. The RasMol Home Page. 2001. [16 December 2005]. http://www.umass.edu/microbio/rasmol/

Martz E. Toobers in Science Education. 2005. [16 December 2005]. http://www.umass.edu/molvis/toobers/

Roberts J. R., Hagedorn E., Dillenburg P., Patrick M., Herman T. Physical models enhance molecular three-dimensional literacy in an introductory biochemistry course. Biochem. Mol. Biol. Educ. 2005;33:105-110.

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A Simple and Effective Protein Folding Activity Suitable for Large Lectures

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This article describes a simple and inexpensive hands-on simulation of protein folding suitable for use in large lecture classes. This activity uses a minimum of parts, tools, and skill to simulate some of the fundamental principles of protein folding. ...

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Data Nuggets | Bringing authentic research and data into K-16 classrooms

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Free activities that bring real scientific data into the classroom, guiding students through the process of science while building their quantitative abilities.

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Application for teacher fellowship courses to Costa Rica, Baja, Hawaii or Yellowstone - pay airfare only if selected -deadline Sept 1, 2018.

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- Develop your familiarity with EPI's approach to education through field science.
- Celebrate and reconnect with the fundamentals of how students learn.
- Provide unique experiences and activities to take back to your classroom.
- Build a supportive network of science educators working towards similar goals.
- Introduce you to EPI's work and promote future student courses to our program sites.

Each professional development program is 8 days in length. On-course fellowship expenses for accepted fellows are subsidized by EPI through scholarship. After scholarship, program fees range from $250 to $600. This program fee is due November 1st and covers all meals, lodging, and activities while on course. EPI works hard to ensure that program fees are not obstacles to participation. When other professional development funds are not accessible to cover program fees, EPI has a limited scholarship pool available to support those who would not be able to attend otherwise. These limited need scholarships are meant to diversify and promote inclusion in the EPI Teacher Fellowship community. Each participant is also responsible for purchasing his/her own round-trip airfare to the designated program city; all other costs are paid by EPI. There is no cost to apply.

Eligibility: Formal and informal educators from any country are welcome to apply. EPI's curriculum is best suited to educators teaching at the middle school, high school, or university level, and applications from these educators are strongly preferred. Applications from educators in any subject area are welcome. At this moment, we are not accepting applications for educators serving elementary students and younger.

Process: 2019's Application Period will open on July 1st and close on September 1st, 2018. Don't wait until the last minute - applications will be reviewed & evaluated in the order they're received.
Meet our 2018 Fellows
Professional development fellowships on offer in 2019:

March 30- April 6, 2019
Focus Areas: Marine Ecosystems; Program Development; Involving Youth in Conservation and Building Sustainable Communities
Baja's Sea of Cortez is a World Heritage Site. While it remains a remarkably rich tropical marine ecosystem, it is slowly being diminished by human impacts, which makes the work of cataloging and studying its marine species a critical task. On course, you'll stay on Espiritu Santo Island, where you'll learn about this fragile ecosystem while participating in and evaluating past and future research projects. You'll also meet local youth and share methods of engaging your students in conservation, at home and abroad.

Yellowstone Wildlife Ecology
April 6-13, 2019; August 10-17, 2019
Focus Area: Wildlife Biology; Conservation Management Practices
EPI partners with the National Park Service to bring students and educators into the park and onto critical research projects that enhance our understanding of wildlife dynamics. You'll work with park research teams on bison and ungulate migration studies (work will vary based on season and conditions).

Costa Rica Sea Turtle Ecology
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Focus Areas: Field Research; Rainforest Ecology
At field sites along the Caribbean coast, EPI works with partner organizations to monitor and protect the incredible and ancient leatherback sea turtle. Working alongside researchers, you will monitor the nesting beaches for adult turtles coming to shore while you learn about the greater systems and ecology that enmesh this critically endangered species.

August 2-9, 2019
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Partnering with local Hawaiian conservation organizations this course will immerse you in the natural beauty of Maui and give you the tools to understand and address critical conservation issues. Your work is rooted in the scientific method as you examine traditional agricultural practices and how native Hawaiian methods of resource management have successfully guided the work of generations of islanders.
Quotes from past fellows:
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"This was unlike any experience I've had before; it was engaging, empowering, positive, thought-provoking, and motivating. I'm so impressed, overall, with the quality of professional development we received.

"The best professional development experience I have had so far! A much needed re-invigoration of my passion for teaching. Also personally an awe-inspiring and fascinating experience. I am so thankful for having been selected for this program. A very positive experience in every sense."

"This experience reminded me of why I love science, why I am the environmental club advisor, and how much I want my students to experience this. This was by far the best course I have ever taken."

"It motivated me to bring more citizen science into my classroom and look for real research opportunities for my students with scientists from local communities."

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EPI's Teacher Fellowship - for High School Teachers

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Develop your familiarity with EPI's approach to education through field science. - Celebrate and reconnect with the fundamentals of how students learn. - Provide unique experiences and activities to take back to your classroom. - Build a supportive network of science educators working towards similar goals.

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2017 JLouis-HMS Review Session I Final (1)

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Great resources for A&P and AP. Hit up "Classes" on the top of the page to drop down to the course of interest.

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The Biology Corner - Resources for Teachers

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Resources for biology students that include worksheets, labs, and student activities. Find everything you need for your biology lessons here!!

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Evolution of bacteria in realtime

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The Evolution of Bacteria on a “Mega-Plate” Petri Dish (Kishony Lab)

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Bonnie Bassler discovered that bacteria "talk" to each other, using a chemical language that lets them coordinate defense and mount attacks. The find has stunning implications for medicine, industry -- and our understanding of ourselves.

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BioTeach teacher professional development programs bring together resources from universities, biotech companies, and veteran educators to provide teachers with the skills and knowledge to implement innovative life sciences labs and develop cutting-edge life sciences curricula. Our BioTeach workshops qualify for professional development points (PDPs) and, in some cases, graduate credit.

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LAB RULES - Dua Lipa "New Rules" Parody | SCIENCE SONGS

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big big ideas and enduring understanding with science practices

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You all had asked about my syllabus for pacing etc...

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You all had asked about my syllabus for pacing etc...

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Nobelprize.org, The Official Web Site of the Nobel Prize

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XKCD Global Temperature Timeli

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xkcd.com is best viewed with Netscape Navigator 4.0 or below on a Pentium 3±1 emulated in Javascript on an Apple IIGS at a screen resolution of 1024x1. Please enable your ad blockers, disable high-heat drying, and remove your device from Airplane Mode and set it to Boat Mode.

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Vernier lab modified for homeostasis in A&P by Brogna

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Honors A&P Homeostasis Lab: Mammalian Diving Response Brogna

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Greg Mulder at Linn-Benton CC and Pat Keefe at Clatsop CC have developed these tools for investigating issues related to global and national energy issues. I thank them for the marvelous work they have done and their willingness to openly share their tools and thoughts with students and other teachers.

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BioGraph is a collaborative, research-based design project created by the Scheller Teacher Education Program and the Graduate School of Education at UPenn. BioGraph improves comprehension of biology by incorporating complex systems ideas (e.g. how birds behave in a flock) into the standard biology curriculum.

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AlleleA1 simulates evolution at a single locus in an ideal population of imaginary organisms. The locus of interest has 2 alleles: A1 and A2. The user enters values for parameters controlling selection, mutation, migration, genetic drift, and inbreeding. As the simulation runs, the software plots a graph showing the frequency of allele A1 over time.

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As part of the KABT thread at the recent KATS KAMP, I argued that we should be asking our students to use spreadsheets to model the concepts of population genetics-in particular Hardy-Weinberg equilibria. I tried to make the case that most of the efforts to model H-W equilibrium in classroom activities such as the AP Biology H-W lab, the M & M's labs or with beans suffer from too small of sample size (population) or are tedious for the students to explore. On the other hand, working up your own models or having students create their own can be a challenge. The benefits to learning are worth the challenge. In this post, I'll present the essential parts of an EXCEL spreadsheet that can be used to explore some of the first principles of the effects of population size on drift. This is not presented as the definitive spreadsheet model but rather a rather simplistic model accessible and modifiable by your students. BTW, it takes longer to read this post than it takes to make this relatively simple spreadsheet. I suggest that you bring up EXCEL or some other spreadsheet in a different window and try to create this worksheet as you follow these instructions. Once you've mastered this and can creat or modify it at will, then try it out with your students-they can handle this level of difficulty. And when do, they will have an effective tool to explore the basic principles of H-W equilibrium-one that they created.

Here's what we are shooting for; the basic spreadsheet model for a 2 allele model:

(I've recently reviewed this and found that I didn't mind my p's and q's-sorry for the error but the technique is the same.)

Like other simulations, this first spreadsheet assumes a sexually reproducing species with an infinite gene pool, limited zygotes, random mating, no selection, no mutation, and no migration. The green zone on this spreadsheet represents the gene pool. Note that the value for is entered in cell"B1″and the value for is calculated by a formula in cell "C1".

Enter the label, "gametes" in cell "C4", the label "zygote" in cell "D4", the label "AA" in cell "E4, the label "Aa" in cell "F4", and the label "aa" in cell "H4"

The gene pool is assumed to be infinite and the selection for gametes for the next generation is assumed to be random. To accomplish this in the spreadsheet we call on the RANDOM function. If you were to pick an empty cell on the spreadsheet and enter the following function: =RAND() you'd get a random number returned that was somewhere between 0 and 1. Try it out and see. Our entire model is based on this RANDOM function and unfortunately I'm not sure how random it really is but for our purposes it will work.

In cell "C5" we will generate a random number, compare it to the value of p, and then place either an "A" gamete or an "a" gamete in the cell.

Note that the function that is entered in cell "C5" is: =IF(RAND()<=B$1,"A","a")

Which basically says, if a random number between 0 and 1 is less than or equal to the value of then put an "A" gamete in this cell or if it is not less than or equal to the value of p put an "a" gamete in this cell. "IF" functions and "RAND" functions are very powerful tools when you try to build models for biology. Now create the same formula in cell "D5". When you have this completed then press the "F9" key on your windows keyboard to force a recalculation of your spreadsheet. If you have entered the functions correctly in the two cells you should see changing values in the two cells.

We'll put the zygotes in cell "E5" . The zygote is a combination of the two randomly selected gametes. In spreadsheet vernacular you want to concantenate the values in the two cells: In cell "E5" enter the function: =CONCANTENATE(C5,D5)

The next columns on the sheet, "F", "G" and "H" are used for bookkeeping-keeping track of the numbers of each zygote's genotype. They are rather complex functions that use nested "IF" functions and also the "EXACT" function. The"EXACT" function is required to determine the difference between "A" and "a". Here goes:

The function in cell "F5" is: =IF(EXACT(E5,$F$4),1,0)

which basically states: if the value in cell "E5" is exactly "AA" then put a 1 in this cell, if not then put a 0.

Enter a very similar function in cell "H5".

which basically states: if the value in cell "E5" is exactly "aa" then put a 1 in this cell, if not then put a 0. (Note that the value "aa" is stored in cell "H5"

Now let's tackle the nested "IF" function. This is needed to test for either "Aa" or "aA"

In cell "G5" enter the nested function: =IF(EXACT(E5,$G$4),1,IF(EXACT(E5,"aA"),1,0))

The example in the image has an extra set of parentheses-something that sometimes happens when I'm trying to nest functions. At any rate this function basically says: if the value in cell ""E5" is exactly equal to "Aa" then put a 1; if not then if the value in cell "E5" is exactly "aA" then put a one; if it is neither then put a 0 in this cell....

There you have it. Copy the cells "C5" through "H5" down for as many zygotes as you'd like in the first generation. Sum up the values in the "F", "G", and "H" columns to summarize the genotype frequencies in the next generation, make a histogram and you end up with something like this:

With a model like this you can vary the number of offspring by inserting or deleting rows to investigate the effect the size of the population has on the gene frequencies in the next generation. Those of you with the AP Biology Lab manual can use this spreadsheet to answer the first few questions in the simulation part of the exercise and it should be pretty easy to modify it to answer others. That's your challenge. Let me know how it works out.

BW

Comments

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As part of the KABT thread at the recent KATS KAMP, I argued that we should be asking our students to use spreadsheets to model the concepts of population genetics-in particular Hardy-Weinberg equilibria.

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Zooniverse- help collect data for real research projects

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Zooniverse- help collect data for real research projects

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Great for ecology population study

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The Zooniverse is the world's largest and most popular platform for people-powered research.

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Do you want to use Gapminder tools in your classroom? Check out all our resources on this page and the downloads page to get started. For more info, contact our educational staff at [email protected] and [email protected] .

Featured examples of Gapminder in education

Teachers TV: Looking at statistics with Year 8 students
[Javascript required to view Flash movie, please turn it on and refresh this page]Thanks to: Bob Lang

Gapminder and Worldmapper
Geography for a changing world resources from the Geographical Association, UK.
Thanks to: Paula Cooper

Gapminder course at the NYC iSchool
An experimental high school course that challenges 10th and 11th grade students to use a quantitive lens to analyze the last 200 years of global history.
Thanks to: Jesse Spevack

Featured resources

External resources about Gapminder

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Do you want to use Gapminder tools in your classroom? Check out all our resources on this page and the downloads page to get started. For more info, contact our educational staff at [email protected] and [email protected] .

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If you scroll down to the "Teachers and Students" Section there is a PDF with lesson plans

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Description

We have recently received a $1M grant from the National Institute on Drug Abuse to develop and implement an educational program called SEADAP (Science Education Against Drug Abuse Partnership) to teach students in grades 6-12 about how commonly abused drugs (e.g. caffeine, sugar, alcohol, nicotine) work in the brain to produce addiction. SEADAP is founded on our extensively published research at Temple University demonstrating that aquatic flatworms called planarians demonstrate addictive-like behaviors to substances such as alcohol, nicotine, caffeine and sugar contained in products (e.g. energy drinks such as Red Bull, coffee, frappuccinos, cigarettes, beer, liquor) that children and adolescents can encounter in their everyday lives. The novelty of SEADAP is that it is the first educational program that uses living animals to teach middle and high school students about the science of drug addiction and hazards of using addictive substances, making it entirely different from past programs such as DARE and Life Skills. The principal investigator of the project, Dr. Scott Rawls, has published 25 peer-reviewed articles demonstrating the scientific relevance of planarians to drugs of abuse, and 11 of those articles were co-authored by local high school students who conducted the research and participated in the publishing process. Planarians have a simple brain and produce chemicals that contribute to addiction in human patients and are ideal for broad-scale learning in a 6-12 environment because they are cheap, easy to use, and amenable to employing hands-on, inquiry-based lesson plans that enable students to quantify actual human-like behavioral responses to drugs of abuse, including dependence, withdrawal, anxiety, tolerance, drug-seeking, relapse, and changes in activity. Our lessons allow students to simulate roles of medical researchers by creating and testing their own hypotheses to study the science that underlies drug addiction. We hope to let students reach their own conclusions through inquiry, experimentation and guided discussions and to spark their interest in biomedical research as a career, expand their understanding of how science is applied in the real world, and educate them about medical, economic and criminal costs of drug abuse.

Funding

Science Education Drug Abuse Partnership Award (SEDAPA): Supported by the National Institute on Drug Abuse (NIDA) and Office of Director (OD) within the National Institutes of Health

Leaders

The program has an appropriate balance of basic science, science education and assessment and is being led by: Dr. Scott Rawls, Principal Investigator, who is a basic scientist, former high school teacher and tenured faculty member at Lewis Katz School of Medicine at Temple University; Dr. Rhea Miles, a science education expert and tenured faculty member at East Carolina University; Kathleen Mooney, an assessment specialist with SERVE out of UNC-Greensboro; and Dr. Sara Ward, a basic scientist at Temple.

Logistics

No financial cost will be imparted to participating schools. The grant provides resources for all lessons, stipends for participating teachers, and funding for substitute teachers if professional development workshops occur on a school day. Teacher commitment includes attending a 2-day professional development workshop in the Feb-April 2015 time frame, subsequent implementation of 1-3 lessons with students in their classrooms, and a 1-day post-implementation and assessment workshop over the summer of 2015. Teachers will be paid a stipend of $200 for the completion of 2 face-to-face workshop sessions, $200 for completed implementation of the SEADAP-developed lesson plan in the classroom, and $100 for the completion of the 1-day post-implementation face to face session over the summer (for a total of $500). The scheduling of the initial 2-day workshops is flexible and can be adjusted to the convenience of teachers (e.g. 2 weekdays from 8-4, a Friday-Saturday combination, or 2-3 long afterschool sessions of 3-8 PM). Workshops can be held at Lewis Katz School of Medicine or at a local school depending on the number of teachers and their preferences.

Workshops will cover key aspects of the program, including presentations about the basic science of drug addiction and pharmacology of drugs of abuse and demonstrations showing effects of drugs of abuse on planarians. Time will also be provided time for teachers to conduct experiments with planarians to begin formulating their lesson plans and designing rubrics (note: we have already developed lesson plans tailored to middle or high school students). Lessons are designed to align with common core and PST standards and can be followed in a "recipe" like fashion, or teachers can use them as a starting point to improvise their own lesson plans using the basic components of the program. Each lesson generally consists of three components: an initial discussion/introduction of background information, a demonstration of the experimentation to the students by the teacher, and actual experimentation by the students. Each component of the lesson should take about 45 minutes of classroom time and can be used to reinforce all core standards in science, technology and engineering education. The assessment component for teachers consists of: a) administering a pre-/post-test to their students to measure increases in student awareness/knowledge, b) allowing SERVE staff to observe student use of planarians in the classroom, and c) providing feedback regarding their experience in the SEADAP program (via surveys, focus groups, and/or interviews).

Publications Related to Planarians

For Teachers and Students

Contact

Scott Rawls, PhD
Principal Investigator
scott.rawls@temple.edu
Office: 215-707-4942

Visit the National Institute on Drug Abuse (NIDA) website for information about drug addiction and commonly abused drugs.

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Science Education Against Drug Abuse Partnership (SEADAP)

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We have recently received a $1M grant from the National Institute on Drug Abuse to develop and implement an educational program called SEADAP (Science Education Against Drug Abuse Partnership) to teach students in grades 6-12 about how commonly abused drugs (e.g. caffeine, sugar, alcohol, nicotine) work in the brain to produce addiction.

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Sumanas, Inc. Animation Development: Biology

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Legal notice: Noncommerical links to animations on this website are permitted only if the link is to the HTML file displaying the animation. Direct links to Flash (.swf) or video (.mov/.mp4) files are expressly prohibited. Links for commercial purposes, or downloading files for offline use is prohibited without the prior written permission of the copyright owner (indicated beneath each animation).

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Statistics & Spreadsheet Lab

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Learn.Genetics [Internet]. Salt Lake City (UT): Genetic Science Learning Center; 2018 [cited 2023 Nov 27] Available from https://learn.genetics.utah.edu/

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Graham Walker, Monitoring Editor

Abstract

This article describes a simple and inexpensive hands-on simulation of protein folding suitable for use in large lecture classes. This activity uses a minimum of parts, tools, and skill to simulate some of the fundamental principles of protein folding. The major concepts targeted are that proteins begin as linear polypeptides and fold to three-dimensional structures, noncovalent interactions drive this folding process, and the final folded shape of a protein depends on its amino acid sequence. At the start of the activity, students are given pieces of insulated wire from which they each construct and fold their own polypeptide. This activity was evaluated in three ways. A random sample of student-generated polypeptides collected after the activity shows that most students were able to create an appropriate structure. After this activity, students (n = 154) completed an open-ended survey. Their responses showed that more than three-quarters of the students learned one or more of the core concepts being demonstrated. Finally, a follow-up survey was conducted seven weeks after the activity; responses to this survey (n = 63) showed that a similar fraction of students still retained these key concepts. This activity should be useful in large introductory-level college biology or biochemistry lectures.

INTRODUCTION

Gaining an understanding of the fundamental principles of protein folding is an important part of most introductory-level undergraduate biology and biochemistry courses. At the introductory level, an appropriate understanding of protein folding would include the following three major concepts:

1. A protein is synthesized as a linear chain of amino acids that then folds into a complex three-dimensional shape.

2. Noncovalent interactions (hydrogen bonds, electrostatic interactions, van der Waals bonds, and hydrophobic interactions) as well as covalent interactions (e.g., disulfide bonds) between different parts of the protein chain drive the folding process.

3. The final folded shape of the protein depends on its amino acid sequence.

Because these concepts involve complex three-dimensional molecules, two-dimensional blackboard and textbook presentations often do not communicate them effectively. Many instructors therefore use supplemental methods, including molecular visualization, and, in some cases, hands-on demonstrations and activities. Molecular visualization (MolVis) software allows the user to achieve a three-dimensional impression by manipulating a two-dimensional image of a particular molecule. There are a large variety of MolVis programs, sites, and tutorials available to educators (e.g., Martz, 2001 Khoo and Koh, 1998 White et al., 2002 Roberts et al., 2005 ). ; ; ); these tools have been shown to be effective for teaching purposes (

As an example of protein folding, I have used molecular visualization presentation of hemoglobin in my lectures for several years ( White et al., 2002 ). During this presentation, I would explain how the protein began as a linear chain and then folded, citing key noncovalent interactions that give the protein its final folded shape. Although I have been pleased with the results, I wanted to find a hands-on physical model that would show how the folding process proceeds rather than working backward from a fully folded protein. I wanted each of the roughly 200 students in lecture to simulate the folding of their own protein so as to get a visual and tactile "feel" for the process. I wanted this activity to show how a linear chain of amino acids can fold into a three-dimensional shape based on interactions between parts of the chain even if the activity did not simulate all of the factors involved in this process. Furthermore, I wanted this activity to fit within the spatial, temporal, and logistic constraints of a 50-min lecture in a typical large lecture hall. Consequently, the activity needed to be inexpensive, require a small number of parts, and require no special tools or accessories.

Research on the efficacy of hands-on modeling of chemical and biological structures has shown encouraging results. There have been several studies ( Howe and Durr, 1982 Copolo and Hounshell, 1995 Barnea and Dori, 1999 Gabel and Sherwood (1980) Roberts et al. (2005) showed that physical models combined with MolVis helped students to learn about protein structure. In their study, students reported that hands-on modeling using rigid models of fully folded proteins was the most helpful mode for teaching these concepts. These results, combined with my experience teaching this material, suggested that using a hands-on activity in lecture would likely be productive. showed that a year-long, model-based chemistry curriculum had improved learning outcomes compared with traditional instruction. ) where use of physical models of simple chemical structures, combined with other innovations, showed increased learning compared with traditional curricula. ; ;

Several hands-on protein folding activities have been developed by others. Martz (2005) recommends using Toobers-long wires wrapped in foam rubber-to simulate protein folding. Others have developed a set of highly realistic activities using Toobers with attached magnetic side chains ( Nelson and Goetze (2004 ) developed an elegant demonstration of protein folding that uses pipe cleaners to simulate the protein chain. However, distributing and assembling the several pipe cleaners, tape, and binder clips required for this activity would not be easy or rapid on the small desks found in most large lecture halls. www.moleculardesigns.com/toobers.php). Unfortunately, although Toobers are relatively inexpensive, it is still prohibitively costly to give each of the 200+ students in lecture a Toober kit of their own.

Given these constraints, I have developed a simple simulation that uses a single piece of wire to simulate a small polypeptide chain. This activity illustrates the three core concepts of protein folding described and can be easily carried out by students in a large lecture class. I have conducted a preliminary evaluation of the activity that shows that it is effective in conveying these concepts.

INSTRUCTIONAL CONTEXT

I use this activity in General Biology I (Bio 111) at University of Massachusetts (Boston, MA). Bio 111 is the first course of a two-semester introductory biology series for biology majors. Bio 111 covers genetics, biochemistry, cell biology, and molecular biology. The course consists of a 50-min lecture three times a week and 10 laboratory sections that meet once a week for 3 h. I give the lectures and supervise the graduate teaching assistants who teach the laboratories.

There are roughly 240 students enrolled in the class in any given semester. The students in Bio 111 are a rather diverse group compared with many introductory-level science courses; about 75% are female, 40% are nonwhite, and their average age is 22 yr. Roughly one-third (29%) are majors in biology-related subjects (biology, biochemistry, premedical), and a similar fraction (35%) are undecided as to their major. For many of these students, 48% of whom are freshmen, this course is their first college science course and their first science course in several years.

I am able to determine the number of students attending each lecture by using the Personal Response System ( www.gtcocalcomp.com/interwriteprs.htm), where each student answers multiple-choice questions in lecture by using an individual infrared transmitter. On the day that I conducted the first phase of the evaluation of this activity, there were 189 students in the lecture hall.

I use this activity during my first lecture on protein structure. Before this lecture, I have introduced basic chemistry as it applies to proteins (covalent and noncovalent bonds) and the idea of polymers. I begin this lecture by talking about amino acid structure-backbone and side chain-and then describe how amino acids are linked to form protein chains. I then discuss, with examples, the different properties of amino acid side chains. Finally, I show them the three-dimensional shape of hemoglobin by using molecular visualization software and explain that proteins have complex three-dimensional folded shapes. This sets up the background for the activity.

LECTURE ACTIVITY

For the activity, each student is provided with a 4-ft length of 18-gauge insulated wire. This wire is available from many sources. 1 In addition, each student receives a handout that explains how to use the wire to simulate a polypeptide chain. This handout can be accessed online in .pdf and .doc format at http://intro.bio.umb.edu/BW/WireDemo.html. These instructions, combined with guidance from the lecturer, are sufficient for the students to perform the activity during the lecture.

First, I explain how their wire will model a short polypeptide chain (as shown in ). The straight part of the wire simulates the backbone, and the loops simulate the side chains. Large open loops (large enough to accommodate two fingers) represent hydrophobic side chains, long closed loops (four twists) represent positively charged side chains, and short closed loops (two twists) represent negatively charged side chains ().

Students are then told to twist their wire to make their own six- to eight-amino acid polypeptide chain. They twist the wire to form loops corresponding to their choices of hydrophobic, anionic, or cationic side chains, leaving three finger-widths of space between each side chain. The simulation works better if they make more hydrophobic side chains than charged side chains and if they also make at least one anionic and one cationic side chain. It takes students ∼3-4 min to twist their wires to produce their linear polypeptides.

At this point, I tell the students that they have just made a simulated short polypeptide. I ask them what they would expect the hydrophobic side chains to do when surrounded by water. Based on our discussions of the hydrophobic effect, they predict that the hydrophobic side chains would cluster in the center of the protein. I tell them to do this with their wires; they then fold their wires into compact three-dimensional structures with the hydrophobic side chains inside. I then ask them what the anionic and cationic side chains would do. When they respond with "form ionic bonds," I tell them to do this with their models as well; they bring the anions to the cations as much as possible while keeping the hydrophobic side chains inside.

At this point, they each have a little ball of wire simulating their fully folded protein. I then ask them the following questions and discuss the answers (in parentheses):

1. What holds your polypeptide in its shape? (Ionic bonds and hydrophobic interactions.)

2. Why is the shape of your polypeptide different from that of your neighbor? (They have different amino acid sequences.)

Finally, I have them simulate thermal denaturation by having them hold their proteins by one part of the backbone and shake them to simulate heating. I explain that this would break the weakest bonds first; that is, the noncovalent bonds. As a result, the proteins then become denatured-they lose their proper folded shape. I explain that this often exposes their hydrophobic side chains to the solvent. The hydrophobic side chains from different molecules can then aggregate-molecules held by neighboring students can link together. I explain that this is what happens when, among other things, egg whites are cooked. We then move on to a molecular visualization-based presentation on an actual protein, hemoglobin. From start to finish, the activity takes roughly 10-12 min.

EVALUATION

The first part of the evaluation was designed to assess the degree to which they understood and followed the directions. I collected a sample of 24 folded wires after the lecture. The majority (19 or 79%) had between six and eight amino acids. Twelve of the 24 "polypeptides" (50%) made by the students had a mixture of hydrophobic, cationic, and anionic side chains; another eight (33%) had hydrophobic and either cationic or anionic side chains. Only four of the 24 (17%) polypeptides had only hydrophobic side chains or were uninterpretable. Overall, 79% had an acceptable structure: six to eight side chains and a mixture of hydrophobic and charged side chains. Several wires from this sample are shown in . The best of these (a) clearly shows the different side chain types; others (, b-d) show some of the mistakes that students made. These mistakes include having more hydrophilic than hydrophobic side chains (b), having only hydrophobic and cationic side chains (c), and not twisting the wire properly (d).

The second part of the evaluation assessed their learning of the three major concepts by using a short anonymous voluntary survey conducted in lecture immediately after the activity. A voluntary survey was chosen for its simplicity of administration; furthermore, response rates to previous voluntary surveys have been high. There were two forms of the survey distributed randomly to the class. These two different surveys were used to approach the students' learning from different perspectives and thereby yield a richer set of responses. Roughly one-half of the students received survey A, which asked the following:

1. What did you learn about proteins from the wire demonstration?

2. What about proteins was still unclear after the wire demonstration was finished?

3. How could the wire demonstration be improved?

The other one-half of the students received survey B, which asked the following:

1. Give one feature of the wire demonstration that accurately simulates the way proteins fold and explain why it is realistic.

2. Give a feature of the wire demonstration that does not accurately simulate the way proteins fold and explain why it is unrealistic.

3. How could the wire demonstration be improved?

There were 82 responses to survey A and 72 responses to survey B. The total of 154 surveys represents 81% of the 189 students in lecture. These responses were then scored based on the three major concepts described previously.

When asked what they had learned from the demonstration (survey A, question 1), 63 responses (77%) mentioned at least one of the major concepts. When asked what was still unclear (survey A, question 2), only 11 (13%) of the responses listed any of the major learning goals. Similarly, 59 (82%) of the responses reported that at least one of the major concepts was represented accurately by the activity (survey B, question 1) and only 11 (15%) of the responses indicated that one of these was not represented accurately by the activity (survey B, question 2).

These results can be further analyzed by the specific type of response, as shown in and . shows the eight most frequent response classes to the questions that asked for what the students learned or what was represented accurately (survey A and B, question 1). The three major concepts are the most frequently given responses. Students' responses also show several other notable learning outcomes including a "feel" for the process and an understanding of the difference between backbone and side chains. shows the eight most frequent response classes to the questions that asked for what was still unclear or not accurately represented by the activity (survey A and B, question 2). Only one of the three learning goals (Concept [2]) is represented in these responses and was only mentioned by three students (4%). The most frequent category of response was that the exercise was fine as it is. These responses also reveal some physical difficulties with the wire and suggest that taking more time with the activity would be productive.

Table 1.

What did you learn about proteins from the wire demonstration? (n = 82)

Give one feature of the wire demonstration that accurately simulates the way proteins fold and explain why it is realistic. (n = 72)

1. 35 (43%) Hydrophobic/hydrophilic interactions. Concept (2).

1. 45 (62%) Hydrophobic/hydrophilic interactions. Concept (2).

2. 32 (39%) Protein folding process. Concept (1).

2. 20 (28%) Protein folding process. Concept (1).

3. 19 (23%) Ionic interactions. Concept (2).

3. 11 (15%) Ionic interactions. Concept (2).

4. 11 (13%) Sequence determines structure. Concept (3).

4. 5 (7%) Backbone versus side chain.

5. 11 (13%) Denaturation.

5. 5 (7%) A tactile or visual ′feel′ for what was going on.

6. 10 (12%) Vague mention of ′proteins′ only.

6. 4 (6%) A protein as a three-dimensional object.

7. 8 (10%) A tactile or visual ′feel′ for what was going on.

7. 3 (4%) Denaturation.

8. 7 (8%) Miscellaneous.

8. 3 (4%) Vague mention of ′proteins′ only.

Table 2.

What about proteins was still unclear after the wire demonstration was finished? (n = 82)

Give a feature of the wire demonstration that does not accurately simulate the way proteins fold and explain why it is unrealistic. (n = 72)

1. 50 (61%) ′Nothing,′ blank, ′all clear.′

Biological issues

2. 14 (17%) Questions beyond the scope of the demonstration.

1. 20 (28%) ′Nothing,′ blank, ′fine,′ etc.

3. 4 (5%) Denaturation.

2. 12 (17%) ′In real life, a protein only folds one way.′

4. 3 (4%) ′How the amino acids are joined by the backbone.′

3. 6 (8%) ′Wire does not show how interactions work.′

5. 3 (4%) Ionic or hydrophobic/hydrophilic interactions. Concept (2).

4. 6 (8%) Issues beyond the scope of the demonstration.

6. 2 (2%) ′I'm not sure-I'm just a little fuzzy.′

5. 5 (7%) ′Real proteins have more amino acids.′

7. 2 (2%) Backbone versus side chain.

6. 4 (6%) ′Folding wire is not like real folding.′

8. 2 (2%) Uninterpretable.

7. 4 (6%) ′It's wire.′

8. 3 (4%) ′Wire does not show structure completely.′

Physical/logistical issues

1. 4 (6%) ′Hard to fold the wire.′

2. 3 (4%) ′Wire too floppy.′

3. 2 (3%) ′Took too short a time.′

Finally, both versions of the survey asked how the activity could be improved. Responses to this question from all 154 surveys were pooled to give Box 1. The majority (52%) of the responses said that the activity was fine as it is. The remainder suggested various improvements to the activity some of which we will adopt in future lectures (clearer instructions and taking more time to explain the activity).

Box 1. Survey responses: suggested improvements:

Improvements (pooled from both surveys; n = 154)

1. 81 (52%) "None," blank, "fine as it is."

2. 13 (8%) "Use more flexible wire."

3. 8 (5%) "Color wire by amino acid properties."

4. 7 (4%) "Spend more time on the demonstration."

5. 5 (3%) "Give clearer twisting instructions."

6. 5 (3%) "Give clearer folding instructions."

7. 4 (2%) "Allow neighbors to attach wires together."

8. 3 (2%) "Explain denaturation more."

The third part of the evaluation measured the longer-term effects of this activity using a follow-up survey conducted at the end of the semester, approximately 7 wk after the activity. This survey was based on survey A, question 1, which asked what students had learned from the activity. To avoid excessive prompting, the follow-up survey questions, shown below, do not mention proteins.

Consider the lecture demonstration from the biochemistry section of the class where you each twisted up a piece of blue wire. As a reminder, the wire is shown below (at greatly reduced scale). (The survey included a reduced version of that only showed the wire; none of the lines or text was included.)

1. Do you remember this demonstration? (circle one) Yes No

2. If you answered "Yes" to (1i), please describe what you remember learning from this demonstration. If "No", go on to (2).

There were 144 students in lecture on the day when I carried out this follow-up evaluation. Of these 144 students, 63 (44%) handed in responses to this voluntary survey. Of the 63 students who responded, 61 (97%) stated that they remembered the activity. Of the 63 responses, 53 (84%) included one or more of the major concepts. A summary of the eight most common responses is shown in Box 2. These data show that Concepts (1) and (2) were represented in a large fraction of the responses. In addition, this survey reveals two new response categories. The first, "Side chain interactions determine structure" is closely related to Concept (3). The second, "Different-shaped loops represent different types of side chains," shows that these students remembered some of the details of the activity.

Box 2. Follow-up survey responses: positive outcomes (n = 63)

1. 35 Hydrophobic/hydrophilic interactions. Concept (2).

2. 29 Protein folding process. Concept (1).

3. 8 Side chain interactions determine structure.

4. 7 Different-shaped loops represent different types of side chains.

5. 6 Ionic interactions. Concept (2).

6. 2 Backbone versus side chain.

DISCUSSION

The results show that this is a highly successful activity. Students were, in general, able to twist the wire as instructed. Immediately after the activity, students listed the three major concepts as having been learned or represented accurately in the majority of their responses; these concepts were mentioned by only a small minority as being unclear or inaccurately represented. The fraction of students mentioning at least one major concept (75-80%) is very high, given the brevity of the activity. Although self-reported measures are not as reliable indicators of learning as formal content-based pre- and postactivity surveys, our design avoids some of the weaknesses of this type of analysis. Because we used open-ended questions where the students had to name the concepts without prompting, this analysis is less susceptible to novelty, "leading the witness," and "pleasing the teacher" effects than if we had used multiple-choice content questions or measures of attitude or satisfaction.

The follow-up study shows that students retained several of the learning goals of the activity for at least 7 wk. However, because of the low response rate, the percentage of students remembering the three major concepts should be viewed as an overestimate of retention, because it is likely that students who remembered the activity would be more likely to return the survey form. Even given these reservations, it is clear that this activity had a lasting impact on the students.

In addition to the effects documented above, this activity has other valuable outcomes. It shows students how proteins fold themselves and that this type of self-assembly is possible: although proteins have complex three-dimensional shapes, they are not stamped out of a mold. It provides a concrete illustration of the protein folding process, rather than the endpoint shown by textbook diagrams and molecular visualization. Finally, the demonstration provides a valuable referent for later lectures. As the course progresses, I am able to refer to the wire demonstration as a concrete example when talking about backbone-side chain issues, folding of other proteins, and side chain interactions.

Although there are many positive outcomes from this activity, it should be noted that this highly simplified model of protein folding can lead to important misconceptions, which may need to be specifically addressed with the students. These misconceptions arise from five features of the activity-simplifications inherent in the wire model of protein structure that have important consequences. First, when students twist the side chains along the length of the wire, this implies that the amino acids are formed out of the same material as the backbone rather than being assembled in order from premade monomers. In addition, it implies that hydrophobic side chains are always larger than charged side chains. Second, the activity does not simulate hydrogen bonds; it would be hard to make five distinguishable kinds of loops, and, with only seven amino acids in the chain, it would be difficult to simulate three different types of interactions. Similarly, the activity does not include the effects of side chain shape or covalent bonds between side chains. Third, it suggests that the formation of a hydrophobic core is always the first step in protein folding. Fourth, because the backbone is "inert" in the activity and the polypeptides are short, it is not possible to demonstrate secondary structure. Moreover, these short polypeptides are also incapable of adopting the range of complex three-dimensional shapes formed by full-length proteins. Finally, the wire does not illustrate the amino and carboxy ends of the protein or the directionality of the backbone. Depending on the level of understanding desired by individual instructors, it will be important to discuss some or all of these issues in the context of further treatment of protein folding. This discussion also could lead to a productive conversation about the role of models in science as well as the illustrative and misleading features of any model. Bearing in mind that this activity is designed as an illustration and to provide a referent for later elaboration, rather than as a complete exposition, it is an effective introduction to protein structure and folding.

Footnotes

¹ Insulated 18-gauge copper wire is available at most hardware stores. I recommend 18-gauge because thinner gauges are too flexible to hold the final folded shape of the protein, and thicker gauges are too stiff to twist into amino acid side chains. Precut 4-ft lengths of this wire (part no. 9504) are available from Advanced Wire and Cable (Xenia, OH) ( www.advancedwire.com) at a cost of $0.30 each (minimum order $50.00). Shorter wires do not allow a sufficient number of amino acids; longer wires are cumbersome and hazardous in a crowded lecture hall.

REFERENCES

Martz E. The RasMol Home Page. 2001. [16 December 2005]. http://www.umass.edu/microbio/rasmol/

Martz E. Toobers in Science Education. 2005. [16 December 2005]. http://www.umass.edu/molvis/toobers/

Roberts J. R., Hagedorn E., Dillenburg P., Patrick M., Herman T. Physical models enhance molecular three-dimensional literacy in an introductory biochemistry course. Biochem. Mol. Biol. Educ. 2005;33:105-110.

# data[].attributes.attachment_link.title
A Simple and Effective Protein Folding Activity Suitable for Large Lectures

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This article describes a simple and inexpensive hands-on simulation of protein folding suitable for use in large lecture classes. This activity uses a minimum of parts, tools, and skill to simulate some of the fundamental principles of protein folding. ...

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Lee Ferguson is a rock star!!

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Here you will find various resources appropriate for teaching AP Biology. Feel free to use what you find here. Should you choose to modify the resources you find, please be sure proper attribution is given. Please note: I do not provide answer keys for activities.

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Macroinvertabrate stream quality lab (biotic index) 

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Macroinvertabrate stream quality lab (biotic index) 

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Learn.Genetics [Internet]. Salt Lake City (UT): Genetic Science Learning Center; 2018 [cited 2023 Nov 27] Available from https://learn.genetics.utah.edu/

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crazy biohacker - crazy good prices on mol bio stuff

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crazy biohacker - crazy good prices on mol bio stuff

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http://www.the-odin.com/pipette/

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For anyone who is familiar using arduino to make lab equipment 

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For anyone who is familiar using arduino to make lab equipment 

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Simplified directions for E. coli insulin factory

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Simplified directions for E. coli insulin factory

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The E coli insulin factory shortened with answer sheet

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GREAT modeling activity for how to make recombinant plasmids (I use pre-pGLO lab)

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GREAT modeling activity for how to make recombinant plasmids (I use pre-pGLO lab)

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I've made a simplified version of this  but use the the templates for restriction enzymes and human DNA and plasmid DNA

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crop technoogy animations

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View the animations by clicking the 'view' links for each animation. You can also download these animations if you are logged in. New users Register free here or existing users Login here

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"Polymerase Chain Reaction (PCR)" Biology Animation Library :: DNA Learning Center

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Polymerase chain reaction (PCR) enables researchers to produce millions of copies of a specific DNA sequence in approximately two hours. This automated process bypasses the need to use bacteria for amplifying DNA.

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STEM Resource Finder | Concord Consortium

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The STEM Resource Finder is a collection of the Concord Consortium's best resources for science, math, and engineering education. Our curated collections offer lesson plans and units for your class based on these resources. All for free!"

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By converting our sims to HTML5, we make them seamlessly available across platforms and devices. Whether you have laptops, iPads, chromebooks, or BYOD, your favorite PhET sims are always right at your fingertips.Become part of our mission today, and transform the learning experiences of students everywhere!

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Walter and Eliza Hall Institute of Medical Research

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2018 The Walter and Eliza Hall Institute of Medical Research. ABN: 12 004 251 423

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AP lab 5 cell respiration procedure packet

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US Department of Commerce, NOAA, Global Monitoring Laboratory

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Global Monitoring Laboratory - Carbon Cycle Greenhouse Gases

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The Global Monitoring Laboratory conducts research on greenhouse gas and carbon cycle feedbacks, changes in clouds, aerosols, and surface radiation, and recovery of stratospheric ozone.

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Other Evolution/Big Idea 1 ideas/activities/practice packets in the "Big Idea 1" folder in the "Evolution Ideas from Casey" subfolder

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Other Evolution/Big Idea 1 ideas/activities/practice packets in the "Big Idea 1" folder in the "Evolution Ideas from Casey" subfolder

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topics- cladogram/phylogenetic tree practice, speciation videos and questions, intro to evolution vocab with HHMI videos

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if you have something great try to put in the folder that it fits best in!

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Hardy-Weinberg Lab and practice HW calc questions

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Hardy-Weinberg Lab and practice HW calc questions

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Hand data for messing with standard deviation

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Hand data for messing with standard deviation