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Using simple manipulatives to improve student comprehension of a complex biological process: Protein synthesis
Article first published online: 29 AUG 2012
Copyright © 2012 Wiley Periodicals, Inc.
Biochemistry and Molecular Biology Education
Volume 40, Issue 5, pages 320–327, September/October 2012
How to Cite
Guzman, K. and Bartlett, J. (2012), Using simple manipulatives to improve student comprehension of a complex biological process: Protein synthesis. Biochem. Mol. Biol. Educ., 40: 320–327. doi: 10.1002/bmb.20638
- Issue published online: 14 SEP 2012
- Article first published online: 29 AUG 2012
- Manuscript Revised: 23 MAY 2012
- Manuscript Received: 21 JAN 2012
- active learning strategies
Biological systems and living processes involve a complex interplay of biochemicals and macromolecular structures that can be challenging for undergraduate students to comprehend and, thus, misconceptions abound. Protein synthesis, or translation, is an example of a biological process for which students often hold many misconceptions. This article describes an exercise that was developed to illustrate the process of translation using simple objects to represent complex molecules. Animations, 3D physical models, computer simulations, laboratory experiments and classroom lectures are also used to reinforce the students' understanding of translation, but by focusing on the simple manipulatives in this exercise, students are better able to visualize concepts that can elude them when using the other methods. The translation exercise is described along with suggestions for background material, questions used to evaluate student comprehension and tips for using the manipulatives to identify common misconceptions.
Understanding biological processes is complicated because they occur in three-dimensional (3D) space, more than one event may occur at the same time, often they involve a complex mixture of molecules that form supramolecular structures, and binding of the various molecular constituents in the proper orientation and stochiometry is critical for specificity and efficiency. Difficulty in comprehending biological processes at the molecular level is further compounded by the fact that students cannot observe the molecules and interactions with their eyes. Educators have used a variety of ways to help students visualize molecular structure and interactions including: computer simulations, physical models, two-dimensional (2D) illustrations, and symbols . Although simple manipulatives are often used in pre-college teaching  they are less commonly used at the college level . Selecting an assortment of means to visualize biological processes is advisable since research has found that using multiple representations can improve student learning, e.g. . Here, I describe an exercise that I developed for an Introductory Cell and Molecular Biology laboratory in which students also perform other exercises to reinforce their understanding of translation.
The exercise is part of a laboratory period where students perform in vitro transcription and translation reactions to produce protein from a recombinant DNA construct. The reactions do not take much time to set up but, depending on the transcription/translation system chosen, the incubation times will total at least 1-2 hours. While the reactions are incubating, students examine physical models, review computer animations that illustrate the process of translation, and perform the exercise described below.
Background Information Supplied to Students
At this point in the semester, students have learned about transcription and translation in the lecture. Major differences between prokaryotes and eukaryotes are discussed, although the emphasis is placed on eukaryotes. During prelab lecture, lab instructors review the major points of transcription and translation that are pertinent to the exercise. Transcription is discussed in more detail in lecture, but is simplified in the exercises for this lab so that a majority of the laboratory time is devoted to the process of translation. As is typical of many processes in biology, translation is broken down into discrete steps to help students better understand the process, although students are reminded that biological processes such as this occur in a much more fluid manner than these steps suggest.
To put these steps in context, animations that were shown during lecture are available for viewing, illustrations of the structure of ribosomes (Fig. 1) and a list of the events of translation (Figs. 2–3) are reviewed, and 3 dimensional physical models are included as part of the lab exercise. Unlike the 2D view of the illustrations, the physical models and manipulatives provide a 3D perspective that serve to remind students that the process takes place in 3D space. The physical models used to supplement the translation exercise can be obtained from the Center for Biomolecular Modeling's Model Lending Library at the Milwaukee School of Engineering . The models are based on the pdb files 1FFK, 1GIY, 1EHZ. Students can use these models to better visualize how the two subunits interact, the position where the tRNA's interact with the ribosome and their orientation with respect to the two subunits, the locations that are considered the A, P, and E sites, and where the newly synthesized protein emerges from the ribosome. If computers are available in the laboratory, students can compare the physical models to the electronic 3D model that they can manipulate with programs such as Cn3D, which is freely available at NCBI , as well as others.
An outline of the steps of translation and photos of the manipulatives are shown in Figs. 2–4. Illustrations of the structure of ribosomes that describe the large and small subunits of the ribosome are reviewed with the students as well as an illustration depicting the A, P, and E sites on the ribosome (e.g., Fig. 1). Students often find it difficult to envision that these sites are tRNA binding sites located on the ribosome. Figure 1, Panel c is an example of an illustration depicting the A, P, and E sites on the large subunit of the ribosome, nevertheless, it is important for students to realize that these sites are created at the interface of the two ribosomal subunits. Showing an illustration of the small subunit with these same sites and demonstrating this with the physical models can help to clarify this concept.
In the translation exercise, students use a variety of common items to symbolize the components involved in translation. To get students thinking about the molecules involved in translation, students are asked to verbally list the required components for the process of transcription and translation. This also reminds them that the two processes are distinct since the processes of replication, transcription, and translation are often blurred in students' minds. For transcription, their list might include: a DNA template which contains a promoter, RNA polymerase, and four ribonucleoside triphosphates. For translation, their list might include: mRNA containing a site for ribosome binding, tRNAs, amino acids, tRNA Synthetases, and ribosomes.
Instructions for the exercise are given in Table 1 and a sample gene is shown in Fig. 5. The supplies are listed in Table 2. In order for the exercise to work effectively, there are several logistics to consider: (1) the gene sequence provided, (2) sizing of the components of the exercise, and (3) position of the transcribed mRNA on the paper strip.
- 1The gene sequence is provided in such a way that the mRNA product will already be oriented 5′ to 3′ when transcribed so that students can translate the mRNA without having to transpose the sequence. Four different DNA sequences are distributed to each table of four students to encourage them to work individually rather than completing the exercise as a group. Students are encouraged, however, to help each other with the concepts and logistics of completing the exercise. To simplify grading and to make it easier to catch problems the students may have as they go through the exercise, the four genes actually have the same protein sequence but differ in their untranslated regions.
- 2Sizing of the various components of the exercise is important for proper alignment. The sizing of the lettering in the gene sequence is designed to fit with the manipulatives chosen. For example, the lettering is sized on the gene sequence so that ultimately a codon will match the width of the anticodon on the clothespin. Also, the size of the ribosome diagram is such that two adjacent clothespins with their anticodons will fit so that adjacent codon-anticodon pairs will lie correctly positioned in the A and P sites.
- 3The instructions indicate that the transcribed mRNA should be written at the bottom of a 1” strip of paper. The reason for this is that to observe the matching of the complementary codon-anticodon pair, there must be sufficient space to clip the tRNA clothespin to the blank area of paper above the sequence. If the paper strip is larger than 1-inch, the codon and anticodon will be further apart, and will not illustrate the base pairing as well.
|Synthesis of RNA requires a number of components including: a promoter, an RNA polymerase, a template, and ribonucleoside triphosphates. If the RNA molecule synthesized is an mRNA, the information it contains can be translated into protein, but the components required for protein synthesis are different. A few essential items are an mRNA containing a ribosome-binding site and coding region, ribosomes, transfer RNAs (tRNAs), amino acids, and tRNA synthetases to attach the amino acids to the tRNAs.|
|1. Obtain a gene sequence from your instructor. Each person at your table should have a different sequence. Record the Gene # on your data sheet.|
|2. Starting at the end of the sequence, transcribe the gene onto a 1 inch wide strip of paper that represents the mRNA. Be sure to write the mRNA sequence along the bottom of the strip of paper. Also, for the following exercise to work, the complementary bases should be directly across from each other, in other words: THE SAME SPACING IN THE LETTERS IS ESSENTIAL. Be careful to use the correct strand and to label the ends.|
|1. See the figure for the illustration of a ribosome and tRNA Synthetase Area. You will also need clothespins, small binder clips, one large binder clip and thin width white label tape.|
|2. On the clamp end of the clothespins and the black portion of each small binder clip, place a small piece of label tape. The clothespins are the tRNAs; the small binder clips are amino acids; the large binder clip is a release factor.|
|3. Locate the first AUG on your mRNA and following along in groups of three, locate each of the codons including your stop codon. Using the genetic code table, complete the table below to organize the information you will need. Remember, the genetic code table is based on the mRNA codon, not the tRNA anticodon.|
|4. Prepare your tRNAs by labeling them with the anticodons that match. Note: In reality, the anticodons might be different because of the wobble base pairing, but write the complementary base that you would expect. You will only need one clothespin for each type of amino acid, even if that amino acid is repeated. Remember: tRNAs can be reused after releasing their amino acid to the growing peptide chain. Now prepare your amino acids by writing the three-letter abbreviation on the tape. You may need more than one of each type of amino acid. Since these are the building blocks for the protein, they cannot be reused.|
|5. Place your tRNAs and amino acids in the tRNA Synthetase Area. Charge each of the tRNAs with the appropriate amino acid. Leave any remaining amino acids there for later.|
|6. Line up your mRNA on the ribosome so that the first AUG is in the P site. Follow each step of translation from the initiation of the polypeptide through its release, recharging your tRNAs as necessary.|
|7. Using the manipulatives to model translation, demonstrate the steps of translation to your instructor.|
|Item type||Features or specific items||Item represents|
|Genetic code table||To look up the amino acid coded for by each codon||NAa|
|Gene Sequence||Be sure to designate which is the template strand||Gene|
|Resulting mRNA must contain an AUGb|
|Manipulatives||Illustration of ribosome and tRNA synthetase areac||NA|
|Clothespinsd, spring loaded style||tRNAs|
|Small binder clipse||Amino acids|
|1 medium binder clip||Release factor|
|Thin width white label tape and marker||NA|
To complete the exercise, students first prepare the components by determining what codons, anticodons and amino acids that they will need (see the table provided for students in the instructions in Table 1). With this information, they label the manipulatives as necessary. Next, students aminoacylate the tRNA's.
Students are asked two questions related to this exercise. First, students are asked to give the sequence of the protein synthesized and to label the ends. Students sometimes do not realize that translation gets its name from the fact that the process converts the information from the language of nucleotide sequence to that of amino acid sequence. Thus, this question not only illustrates the directionality of these molecules, but also drives home the point that these are different molecules. Second, students are asked to draw an illustration of the ribosome with its associated tRNA's including the amino acids and/or growing peptide chain at a specified moment during translation. Once they understand the steps of translation and go through the exercise, they should be able to connect the following concepts:
- 1The position of the tRNAs on the mRNA informs us of the amino acids attached to them. For example, when a tRNA is attached to the 3rd codon, the 3rd amino acid in the sequence is the one attached to the tRNA.
- 2The location of the tRNAs and the peptide can be determined by the position of the ribosome on the mRNA, along with the step of translation (i.e., if peptide bond formation and translocation has occurred). This information indicates: in which binding site the tRNA will be located, to which tRNA the growing peptide will be attached, and how many amino acids will be found in the growing peptide chain. For example, if the third codon is in the P site, the peptide bond has just formed, and translocation has not yet occurred, then the first four amino acids will be attached to the tRNA located in the A site and the tRNA in the P site will be deacylated.
Figure 6 shows an illustration that a student might draw to demonstrate the answer to this problem. If you look to the next step, once translocation occurs, the 4th codon will be in the P site, the four amino acids would still be attached to the tRNA, and the A site would be awaiting an aminoacylated tRNA. You can have students “prove” their answer by showing you it is correct with the manipulatives. This further demonstrates their understanding and allows the instructor to correct any misconceptions. Of course, the process is more fluid than these discrete steps, but as pointed out above, this helps students to break the process down. I have found that watching the animations reminds them of the fluidity of the process. Some other concepts illustrated by the exercise are:
Aminoacylation is Critical for Translation to Occur
Students sometimes do not realize that different processes in the cell affect each other and are potential sites of regulation. In the exercise, students must aminoacylate the tRNAs before they can be used in translation. You can point out that translation could not continue without this important step ongoing.
Aminoacylation Does Not Occur on the Ribosome
Students aminoacylate the tRNAs in the “tRNA Synthetase Area” (Fig. 4A). Although a discrete location for aminoacylation has not been reported, the exercise illustrates that it does not occur on the ribosome but elsewhere in the cell.
Relationship Between the Genetic Code, the Components of Translation and the Final Product
Common exercises require students to look up the amino acids that correspond to a series of codons and most students can do this successfully, yet I find that when students are given an anticodon, they do not know how to determine which amino acid to attach to the tRNA. In this exercise, students are able to see the relationship between the codon of the mRNA, the anticodon of the tRNA and the amino acids.
Protein Secondary Structure Forms Quickly After Synthesis
I have noticed that most students attach the binder clips together on the same side so that the peptide looks as if it has some type of secondary structure. I will often use this to briefly discuss protein folding.
Identifying Common Misconceptions
As students are working through the exercise, it is often possible to identify and correct common misconceptions. Examples of corrections of misconceptions include the points given below.
“Stop” and “Start” Are Instructions the Codons Provide for the Ribosome. Start, But Not Stop, Also Specifies an Amino Acid
As indicated above, students are asked to give the sequence of the protein which is synthesized. Including “stop” as the final amino acid in the sequence is a common error, as well as omitting methionine or writing the word “start” or “start-met” for the first amino acid. This provides an opportunity to point out to students the difference between “instructions” and incorporation of amino acids. The Stop codon is an instruction and is not recognized by a tRNA. Instead, a release factor recognizes the stop codon and does not carry an amino acid. Although release factors have structural similarities to tRNAs, they are distinct. The start codon is an instruction and is recognized by a tRNA carrying an amino acid, so this codon is more than an instruction. The methionine carried by the initiator tRNA is incorporated into the protein. An analogy that often helps is to think of the structure of a sentence. The capital letter on the first word is an instruction that the sentence is beginning. We read the first word of the sentence just like AUG is read and specifies methionine. The period at the end of a sentence is an instruction that we have reached the end of the sentence, but we do not read the period out loud just like the stop codon does not specify an amino acid.
The Genetic Code Table Is Based on Codons
Decoding tables are used to uncover messages that are coded. Students often do not understand that genetic code tables are based on the relationship between codons and amino acids. If one has the anticodon, it is not possible to look up the amino acid directly in the genetic code table. Converting from the anticodon to the codon allows the corresponding amino acid to be identified from a genetic code table. Along with this, you can emphasize to students that the codons, anticodons and amino acids are on three distinct molecules. Codons do not appear in the protein sequence nor are they found on the tRNA.
During Translocation, tRNAs Do Not Move Along the mRNA
While doing the exercise, students often try to unclip the tRNAs and move them along the mRNA. Correcting this misconception drives home the point that the mRNA and tRNA are specifically interacting through complementary base pairing of their codon-anticodon pairs and that the tRNAs do not “walk” along the mRNA as they participate in translation. During translocation, the tRNA/mRNA pair moves with respect to the ribosome. Since this occurs in 3D space, what is important is the relationship between these entities rather than which moves.
At first, students think using simple manipulatives is an elementary exercise and question its value. As they complete the exercise, they realize that these simple items that symbolize key components of the translational machinery, make the entire process clearer, and they become less resistant. During the laboratory period, students are also performing in vitro transcription and translation reactions. Since students are unable to see what is happening in the tubes as the DNA template is transcribed into mRNA and the mRNA is translated into protein, this exercise helps them to visualize what is happening during the incubations.
Assessment of Learning Gains
Although a great deal of anecdotal evidence suggested that the exercise improves student understanding of the concepts of translation, to more formally determine these gains, a pre- and postassessment were created to compare students' understanding after reading the textbook sections on the subject of protein synthesis and after the laboratory exercise. The assessment questions are shown in Supporting Information A and the concepts assessed are listed in Table 3. A rubric and answers are shown in Supporting Information B. Pre- and postassessments for each individual were evaluated by their laboratory instructor and the scores were compared using a paired T-test or Chi Square test, as appropriate (Table 4). To minimize bias caused by “teaching to the test”, no laboratory instructor (except the first author of this paper who wrote the assessment questions and only taught one laboratory section) saw the assessment questions before the postassessment was completed by the students.
|1–3||Correspondence between the codon, antidocodon and amino acid as well as the relationship between the position of the ribosome on the mRNA.|
|4||Movement of the various components (tRNA, amino acids and growing peptide chain, ribosome) with respect to one another.|
|5||Understanding codons that specify amino acids, instructions, or both and what constitutes a protein sequence.|
|6||Correspondence between the codon, antidocodon and amino acid. Use of the genetic code table.|
|7||Same as Question #6 plus: How to do the reverse complement. This was not tested by Question #6 since the anticodon given is symmetrical.|
|8||Relationship between codons and protein sequence.|
|9||Recognition of the stop codon.|
|10||Use of the genetic code table.|
|11||The process of translation and movement of the various molecular components.|
|Question||Average scorea, b, c||P-valuesd, e|
On Wednesday of the week before the laboratory exercise, students were instructed to read the appropriate sections of the textbook and were given the preassessment during the next class period. Nine sections of the laboratory meet from Monday through Thursday and are taught by eight different instructors. Although material related to translation was covered during the Monday and Wednesday lecture of the course, there was no significant difference for questions #1 through #10 between lab instructors (ANOVA, Tukey HSD Multiple Comparisons, α = 0.05) suggesting that the major contributor to an improvement in the post-assessment was the exercise and not material covered during the lecture. There was a significant difference (p = 0.038) for question #11 only between the lab sections that meet at 6pm on Wednesday and at 2pm on Thursday. Since lecture meets before 2pm on Monday, Wednesday and Friday, this difference cannot be attributed to an improved understanding of the concepts evaluated on the post-assessment from the lecture. The difference may be due to differences between the two laboratory instructors or the level of students in these two lab sections.
Comparison of the scores for all eleven questions indicated a significantly higher score on the postassessment (Table 4). When individual questions were evaluated, there was a significant improvement for each question as well. Since questions #1-10 were multiple choice questions, they were scored as incorrect (0) or correct (1), so the values in Table 4 for before or after represent the proportion of students that selected the correct answer. Some of the questions were designed to assess the same concept, but there were differences in the level of difficulty that are represented by the scores. For example, Questions #1-3 were designed to test the ability of students to understand the correspondence between the codon, anticodon and amino acid as well as the relationship between the position of the ribosome on the mRNA using a single diagram (see Supporting Information A). Nevertheless, the difficulty increases from #2 (a single amino acid attached to its cognate tRNA) to #3 (an amino acid attached to the tRNA that is carrying the growing peptide chain: requires a student to infer which of the attached amino acids to use) to #1 (an amino acid in the middle of the peptide: requires a student to infer an earlier event). The students selecting the correct answer went from 90% to 77% to 76% as the difficulty increased. In addition, as described below, more students were able to answer the simpler questions even before doing the exercise. Another example is Questions #6 and #7, which both evaluated the ability to use a genetic code table and the correspondence between codons, anti codons and the amino acid. Since the anticodon given was written 5′ to 3′, students would have to find the reverse complement to know the codon for #7. This was not necessary for #6 because the anticodon given was symmetrical. Thus, the lower score for #7 seems to be due to the students either not noticing or not understanding that they needed to consider the orientation of the anticodon.
As noted in Table 4, the comparison made for the statistical analysis was “improvement” versus “no improvement”. Since a student that understood the concept before the exercise would not be able to improve, they were excluded from the analysis. In order to better look at what group this represented, Table 5 separates students into each of the possible four learning categories (see an explanation in Table 5). Although there are many interesting trends that can be gleaned from this table, a few are described in the following two paragraphs.
The last column in Table 5 (i.e., Learning Category 1-1) provides an estimate of those that understood the concept before they completed the exercise. For example, a high proportion of the students (48.6%) understood that the genetic code table represented a 3-letter code found on the mRNA (Question #10). We have not determined in this study if students understood the concept before taking this course, based on reading the textbook, or from information covered in the lecture. Another example can be seen with Questions #1-3 that represent different levels of difficulty for the same concepts (difficulty level: #1 > #3 > #2). Even before the exercise, a higher proportion of the class (40.5% and 48.6%) understood the correlation of the amino acid to the codon when the amino acid was still bound to its cognate tRNA (Question #2 and #3) than the more difficult concept of predicting the codon based on the position in the peptide chain (Question #1, 22.3%). This information can help us to better decide which concepts may need the most attention during the lab.
Based on the first three columns, we can see what proportion of the group learned the concept and what proportion did not learn the concept. For example, Question #4 has the lowest proportion of students (30.5%) that understood the concept at the end of the exercise. Based on this assessment, we can either place more emphasis on those concepts which students continue to struggle with or plan to spend time on the concept during Supplemental Instruction Sessions .
Extensive educational research has demonstrated that student learning improves when students are actively engaged. In our introductory Cell and Molecular Biology lab, one laboratory period is used to reinforce the concepts of translation that are taught in the lecture. Students actively engage in several complementary exercises. An exercise using simple manipulatives to represent complex molecules has proven a useful addition to more common laboratory exercises that include wet lab experiments, molecular models and comparison with two dimensional illustrations. As is expected for students with different learning styles, some students begin to understand the process after doing this exercise, some after reading the textbook, some after manipulating the 3D models, so this exercise provides a complementary means to improve student understanding of the process. Furthermore, as research has shown , the combination of multiple representations will likely improve student learning of the concepts no matter what their learning style. This simple exercise not only helps students to understand the process, but aids instructors in identifying students with common misconceptions. Since the supplies are inexpensive and consist of readily available items, this exercise is accessible to any course interested in using it to improve students' understanding of translation.
The authors would like to thank Dr. Michelle Suhan Thomas for critical review of the manuscript.
- 21999) Using manipulatives in the classroom. Principal, March, 53–57.(
- 5Model Lending Library, Center for Biomolecular Modeling, Milwaukee School of Engineering: Available at: http://cbm.msoe.edu/teachRes/library/index.html.
- 7The International Center for Supplemental Instruction, University of Missouri-Kansas City: Available at: http://www.umkc.edu/cad/si/ publications.shtml.
Additional Supporting Information may be found in the online version of this article.
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