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A Simple Wooden Ribosome Model: Helping Students Understand Transpeptidation

    Author: Donald A. Klein1,*
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    Affiliations: 1: Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523
    AUTHOR AND ARTICLE INFORMATION AUTHOR AND ARTICLE INFORMATION
    • Published 20 December 2010
    • *Corresponding author. Mailing address: Department of Microbiology, Immunology and Pathology, 1682 Campus Delivery, Colorado State University, Fort Collins, CO 80523-1682. Phone: (970) 491-6947. Fax: (970) 491-1815. E-mail:donald.klein@colostate.edu.
    • Copyright © 2010 American Society for Microbiology
    Source: J. Microbiol. Biol. Educ. December 2010 vol. 11 no. 2 172-174. doi:10.1128/jmbe.v11i2.207
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    Abstract:

    In teaching biology, it is critical to communicate broad concepts before considering more specific details of a process. This is particularly important when attempting to communicate the essence of transpeptidation, a key process in translation. Based on my experience in teaching general microbiology, transpeptidation is the most difficult aspect of translation for students to understand.

    Typically, figures given in microbiology and biochemistry texts show movement of the nascent peptide attached to the P position t-RNA to the incoming single amino acid attached to the A position amino acid-tRNA by the use of arrows, an approach that makes it difficult to understand the dynamic aspects of this process. To attempt to improve understanding of this process, tutorials also are available that emphasize decoding “messages” and the use of “Do-it-Yourself DNA Kits” where the process of transpeptidation is not specifically discussed. The simple model described in this communication provides a clear demonstration of the transpeptidation process.

Key Concept Ranking

Amino Acids
0.66751635
0.66751635

References & Citations

1. Brakmann S 2010 Single-molecule analysis: a ribosome in action Nature 464 987 988 10.1038/464987a 20393548 http://dx.doi.org/10.1038/464987a
2. Flammer L 2004 Say it with DNA: protein synthesis tutorial Available from: http://www.indiana.edu/~ensiweb/connections/genetics/dna.les.html.
3. Holoweski D, Quist C 2010 Delicious DNA: transcription and translation simulation using an edible model Available from: http://teacherknowledge.wikispaces.com/DNA+Demonstration+Lesson+Plan
4. Rogerson AC, Cheney RWJr 1989 A physical model illustrating protein synthesis on the ribosome The Am Biol Teacher 51 29 31 10.2307/4448834 http://dx.doi.org/10.2307/4448834
5. Vanzi F, Vladimirov S, Knudsen CR, Goldman YE, Cooperman BS 2003 Protein synthesis by single ribosomes RNA 9 1174 1179 10.1261/rna.5800303 13130131 http://dx.doi.org/10.1261/rna.5800303
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/content/journal/jmbe/10.1128/jmbe.v11i2.207
2010-12-20
2017-09-21

Abstract:

In teaching biology, it is critical to communicate broad concepts before considering more specific details of a process. This is particularly important when attempting to communicate the essence of transpeptidation, a key process in translation. Based on my experience in teaching general microbiology, transpeptidation is the most difficult aspect of translation for students to understand.

Typically, figures given in microbiology and biochemistry texts show movement of the nascent peptide attached to the P position t-RNA to the incoming single amino acid attached to the A position amino acid-tRNA by the use of arrows, an approach that makes it difficult to understand the dynamic aspects of this process. To attempt to improve understanding of this process, tutorials also are available that emphasize decoding “messages” and the use of “Do-it-Yourself DNA Kits” where the process of transpeptidation is not specifically discussed. The simple model described in this communication provides a clear demonstration of the transpeptidation process.

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Figures

Image of FIGURE 1

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FIGURE 1

t-RNA units. A single larger finishing nail is inserted in the center top of the block, for placement of the “amino acid,” and three finishing nails are inserted into the bottom, representing the triplet codon. The size bar is 6 inches in length.

Source: J. Microbiol. Biol. Educ. December 2010 vol. 11 no. 2 172-174. doi:10.1128/jmbe.v11i2.207
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Image of FIGURE 2(a)

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FIGURE 2(a)

The “mRNA” with different colors representing the different amino acids. On the left side, an “I” is used to note initiation sequences and, on the right, “T” for termination sequences. The size bar is 6 inches in length.

Source: J. Microbiol. Biol. Educ. December 2010 vol. 11 no. 2 172-174. doi:10.1128/jmbe.v11i2.207
Download as Powerpoint
Image of FIGURE 2(b)

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FIGURE 2(b)

An end view of the “mRNA” showing the position of the alignment piece that locks the mRNA into the ribosome. The size bar is 6 inches in length.

Source: J. Microbiol. Biol. Educ. December 2010 vol. 11 no. 2 172-174. doi:10.1128/jmbe.v11i2.207
Download as Powerpoint
Image of FIGURE 3(a)

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FIGURE 3(a)

Basic profile of the ribosome model. This is cut to illustrate the 50S and 30S subunits of the ribosome. The size bar is 6 inches in length.

Source: J. Microbiol. Biol. Educ. December 2010 vol. 11 no. 2 172-174. doi:10.1128/jmbe.v11i2.207
Download as Powerpoint
Image of FIGURE 3(b)

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FIGURE 3(b)

End view of the ribosome model showing the base, a short length of 2 by 4, the backboard, and the two-part facing board with the slot to allow the mRNA to move across the face of the “ribosome.” The lower 2 inch by 2 inch piece holds the “mRNA” in place. The size bar is 6 inches in length.

Source: J. Microbiol. Biol. Educ. December 2010 vol. 11 no. 2 172-174. doi:10.1128/jmbe.v11i2.207
Download as Powerpoint
Image of FIGURE 4

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FIGURE 4

The individual amino acids are beverage coasters; on the left, the reverse side is shown. On the reverse, a short piece of rigid plastic tubing is glued to the bottom and a piece of round stick from a swab extends above the top of the coaster approximately 1.5 inches, to allow the amino acids to be “stacked.” The size bar is 6 inches in length.

Source: J. Microbiol. Biol. Educ. December 2010 vol. 11 no. 2 172-174. doi:10.1128/jmbe.v11i2.207
Download as Powerpoint
Image of FIGURE 5

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FIGURE 5

The complete ribosome, with the mRNA in place, and the tRNAs and nascent peptide after two transpeptidation steps have been carried out. The locations of the tRNA on the A, P and finally the E site are noted. The size bar is 6 inches in length.

Source: J. Microbiol. Biol. Educ. December 2010 vol. 11 no. 2 172-174. doi:10.1128/jmbe.v11i2.207
Download as Powerpoint

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