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Journal club as a supplement to the undergraduate biochemistry laboratory
Biochemical Education 28 (2000) 71}73
Journal club as a supplement to the undergraduate biochemistry laboratory Mona L. Hall, Adele J. Wolfson* Department of Chemistry, Wellesley College, Wellesley, MA 02481, USA Received 24 September 1999; accepted 25 October 1999
Abstract After puri"cation of lysozyme, our biochemistry students write a research proposal that outlines a strategy for studying this enzyme after alteration by site-directed mutagenesis. Despite a literature search that yielded a wealth of background information, students were often overwhelmed by the assignment because they were not familiar with advanced techniques of protein analysis. We therefore developed a series of `journal clubsa in which teams of students present methods and data found in papers dealing with lysozyme. The "ve topics for journal clubs include; substrate binding and mechanism; spectroscopic techniques; stability analysis; two-dimensional NMR; and X-ray crystallography. After the adoption of the group talks, the quality of the research proposals improved immensely and students found the assignment to be an educationally rewarding exercise. ( 2000 IUBMB. Published by Elsevier Science Ltd. All rights reserved.
1. Introduction We have previously described a project-based laboratory to accompany the "rst semester of biochemistry [1]. The protein chosen as the object of study for the laboratory is the enzyme lysozyme, and students carry out three projects of increasing complexity over the course of the semester. The third project is a theoretical exercise, a research proposal on protein design by mutagenesis. Each student proposes a mutational study of lysozyme to address a particular question on stability, mechanism, binding, or folding. We found that, although the students had an appreciation of the complexities of protein structure and experimental design, they were not well-equipped to select or describe the methods that would be most appropriate to characterize their mutant lysozymes. There is not su$cient time in the lecture or laboratory portion of the course to cover all of these methods in depth. We therefore developed a journal club assignment as a supplement to lab and lecture. In addition to teaching protein methods, this format has the added advantage of providing opportunities for oral presentation and collaboration. The educational goals of the entire project, with journal clubs, are: (1) to
* Corresponding author.
familiarize biochemistry students with methods of protein analysis in two phases: journal club presentations and research proposal; (2) to have students develop oral presentation skills by presenting topics from the articles and then later by presenting their research proposal; (3) to use the peer review process in order to improve the quality of student work; and (4) to have students develop scienti"c writing skills.
2. Format Students work in teams of four or "ve to present a topic on protein analysis, and each team member has 10 min for her presentation (40}50 min total per group). The "rst team member introduces a method of protein analysis. References from general texts [2}5] are used to learn about the applied methods and some "gures may be used from such sources. The remaining team members present data generated by such a method(s) about lysozyme. Since an entire journal article cannot be adequately discussed in 10 min the talks are limited to only a portion of the data in a given article. Students focus on suggested "gures, graphs or tables. The presentation of research data includes: the experimental goal(s) of the study; location of the amino acid mutation; explanation of the results; and conclusions made from the presented data. In
0307-4412/00/$20.00 ( 2000 IUBMB. Published by Elsevier Science Ltd. All rights reserved. PII: S 0 3 0 7 - 4 4 1 2 ( 9 9 ) 0 0 1 3 5 - 1
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M.L. Hall, A.J. Wolfson / Biochemical Education 28 (2000) 71}73
Table 1 Example of a journal club topic
Table 2 Form for evaluation of journal club presentations
Topic 2: Spectroscopic Techniques Topic for individual student Literature reference
The following evaluation worksheet outlines the requirements for a wellprepared presentation: Ratings (1"well done; 2"good; 3"acceptable; 4"needs improvement) A. Introduction Experimental goals were well de"ned or Methods were clearly described Amino acid mutation was de"ned as: }}} B. Data presentation Figures were adequately used for clarity Methods speci"c to the paper were explained at an appropriate level (more detailed for "rst talk, or reviewed in a subsequent talk) C. Conclusion Signi"cance of the results were summarized or Methods were summarized to introduce subsequent talks D. Overall presentation The presentation was easy to follow and informative The pace of the presentation held audience's interest (neither hurried nor too slow) The presentation was not read but demonstrated a polished knowledge of the topic E. Group dynamics Flow from the previous talk was maintained Presented material was nto redundant A clear relationship was maintained throughout and a cohesive topic was presented
1. Use of #uorescence to probe An overview the location of aromatic residues 2. Changes in the environment Muraki et al. [6] Fig. 5, Table 3 of active site Trp residues due to mutations and substrate binding 3. pK determination of Glu-35 Inoue et al. [7] Figs. 4, 6 ! via Trp-108 absorbance 4. Determination of dissociaDahlquist et al. [8] Figs. 1, 2 tion constant (derive equation) 5. Circular dichroism: an An overview analysis of secondary structure and analysis of thermostability
order to prepare a clear and concise presentation, students are encouraged to use "gures and an outline format to summarize procedures, results or conclusions. The team is instructed to meet several times so that the members can critique content and clarity of the individual's presentation. Furthermore, such preparation in teams ensures that the #ow between presentations is cohesive and the content not redundant. Journal club articles are organized into the following categories: (1) substrate-binding and mechanism; (2) spectroscopic techniques, including #uorescence and circular dichroism; (3) nuclear magnetic resonance; (4) X-ray crystallography; (5) stability analysis by thermal denaturation. An example of one of these topics, spectroscopy, and the papers selected to illustrate its uses, is given in Table 1. An outline of the criteria for evaluation of the oral presentation is given in Table 2. Since we adopted the supplementary journal club, the quality of research proposals has improved tremendously. Students are able to understand the principles of a variety of physical and chemical techniques for characterization of proteins, and utilize these in preparing their proposals. The research proposal includes the following sections adapted from granting-agency guideliness: summary, prior results, project description, and references. The proposal itself and the peer review process have been described [1]. We have modi"ed the peer review form to provide more guidance to the student reviewers, specifying the desired level of detail, appropriate audience level, requirements for tables and "gures, etc. The guidelines for the project description, which is the core of the proposal, are given in Table 3. Evaluation sheets such as those used for oral presentation and peer review clarify expectations and improve the quality of both the work and the review process.
Table 3 Peer review form for evaluation of research proposal (research project only) Peer evaluation of the xrst draft Directions: For each entry indicate: a. Yes, if this item has been completely addressed b. No, if this item must be corrected, then indicated on what page(s) you have placed the relevant comments c. Additional comments should be made on the reverse side of the form Project description YES/NO (comments on page}}}) 1. Opening statements: are concise are not redundant with the summary 2. Methods to be employed: are presented in a logical order are relevant to the purpose of the study explore all the possible outcomes of the mutation are su$ciently described to understand key steps in the procedure are not as detailed as a Methods section are explained at a level appropriate for scienti"c peers are appropriately referenced 3. Previous studies are mentioned: to support the use of the methods to predict possible outcomes are interpreted as possible outcomes and not certain outcomes are relevant and not just space "ller 4. The information from multiple sources does not dominate the discussion. Estimate the percentage of text dedicated to their proposed work vs. previous studies (65}75% for the proposed work is desirable.) 5. The concluding paragraph: "nishes with a strong summary of your study's goals suggests future work
M.L. Hall, A.J. Wolfson / Biochemical Education 28 (2000) 71}73
3. Conclusions Journal clubs are a familiar format for most scientists, but they are not often seen by undergraduate students. One of the great bene"ts of this exercise is that students are responsible for their own learning; they are provided with a starting place but must work to understand the topic and "nd the best ways to present it to their peers. We have found it to be very successful for a course with an emphasis on methods, but it may be easily adapted to many advanced undergraduate courses.
References [1] A.J. Wolfson, M.L. Hall, T.R. Branham, An integrated biochemistry laboratory, including molecular modeling, J. Chem. Edu. 73 (1996) 1026}1029.
73
[2] T.E. Creighton, Proteins: A Practical Approach, Oxford Press, New York, 1989. [3] I.D. Campbell, R.A. Dwek, Biological Spectroscopy, Benjamin/Cummings, Menlo Park CA, 1984. [4] R.A. Bradshaw, M. Purton, Proteins: Form and Function, Cambridge University Press, New York, 1990. [5] Branden, J. Tooze, Introduction to Protein Structure, Garland Publishing, New York, 1991. [6] M. Muraki, K. Harata, Y. Jigami, Dissection of the functional role of structural elements of tyrosine-63 in the catalytic action of human lysozyme, Biochemistry 31 (1992) 9212}9219. [7] M. Inoue, H. Yamada, Yasukochi, R. Kuroki, T. Miki, T. Horiuchi, T. Imoto, Multiple role of hydrophobicity of tryptophan-108 in chicken lysozyme: Structural stability, saccharide binding ability, and abnormal pK of glutamic acid-35, Biochemistry 31 (1992) ! 5545}5553. [8] F.W. Dahlquist, L. Jao, M. Raftery, On the binding of chitin oligosaccharides to lysozyme, Proc. Nat. Acad. Sci. (USA) 56 (1966) 26}29.
Journal club as a supplement to the undergraduate biochemistry laboratory Mona L. Hall, Adele J. Wolfson* Department of Chemistry, Wellesley College, Wellesley, MA 02481, USA Received 24 September 1999; accepted 25 October 1999
Abstract After puri"cation of lysozyme, our biochemistry students write a research proposal that outlines a strategy for studying this enzyme after alteration by site-directed mutagenesis. Despite a literature search that yielded a wealth of background information, students were often overwhelmed by the assignment because they were not familiar with advanced techniques of protein analysis. We therefore developed a series of `journal clubsa in which teams of students present methods and data found in papers dealing with lysozyme. The "ve topics for journal clubs include; substrate binding and mechanism; spectroscopic techniques; stability analysis; two-dimensional NMR; and X-ray crystallography. After the adoption of the group talks, the quality of the research proposals improved immensely and students found the assignment to be an educationally rewarding exercise. ( 2000 IUBMB. Published by Elsevier Science Ltd. All rights reserved.
1. Introduction We have previously described a project-based laboratory to accompany the "rst semester of biochemistry [1]. The protein chosen as the object of study for the laboratory is the enzyme lysozyme, and students carry out three projects of increasing complexity over the course of the semester. The third project is a theoretical exercise, a research proposal on protein design by mutagenesis. Each student proposes a mutational study of lysozyme to address a particular question on stability, mechanism, binding, or folding. We found that, although the students had an appreciation of the complexities of protein structure and experimental design, they were not well-equipped to select or describe the methods that would be most appropriate to characterize their mutant lysozymes. There is not su$cient time in the lecture or laboratory portion of the course to cover all of these methods in depth. We therefore developed a journal club assignment as a supplement to lab and lecture. In addition to teaching protein methods, this format has the added advantage of providing opportunities for oral presentation and collaboration. The educational goals of the entire project, with journal clubs, are: (1) to
* Corresponding author.
familiarize biochemistry students with methods of protein analysis in two phases: journal club presentations and research proposal; (2) to have students develop oral presentation skills by presenting topics from the articles and then later by presenting their research proposal; (3) to use the peer review process in order to improve the quality of student work; and (4) to have students develop scienti"c writing skills.
2. Format Students work in teams of four or "ve to present a topic on protein analysis, and each team member has 10 min for her presentation (40}50 min total per group). The "rst team member introduces a method of protein analysis. References from general texts [2}5] are used to learn about the applied methods and some "gures may be used from such sources. The remaining team members present data generated by such a method(s) about lysozyme. Since an entire journal article cannot be adequately discussed in 10 min the talks are limited to only a portion of the data in a given article. Students focus on suggested "gures, graphs or tables. The presentation of research data includes: the experimental goal(s) of the study; location of the amino acid mutation; explanation of the results; and conclusions made from the presented data. In
0307-4412/00/$20.00 ( 2000 IUBMB. Published by Elsevier Science Ltd. All rights reserved. PII: S 0 3 0 7 - 4 4 1 2 ( 9 9 ) 0 0 1 3 5 - 1
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M.L. Hall, A.J. Wolfson / Biochemical Education 28 (2000) 71}73
Table 1 Example of a journal club topic
Table 2 Form for evaluation of journal club presentations
Topic 2: Spectroscopic Techniques Topic for individual student Literature reference
The following evaluation worksheet outlines the requirements for a wellprepared presentation: Ratings (1"well done; 2"good; 3"acceptable; 4"needs improvement) A. Introduction Experimental goals were well de"ned or Methods were clearly described Amino acid mutation was de"ned as: }}} B. Data presentation Figures were adequately used for clarity Methods speci"c to the paper were explained at an appropriate level (more detailed for "rst talk, or reviewed in a subsequent talk) C. Conclusion Signi"cance of the results were summarized or Methods were summarized to introduce subsequent talks D. Overall presentation The presentation was easy to follow and informative The pace of the presentation held audience's interest (neither hurried nor too slow) The presentation was not read but demonstrated a polished knowledge of the topic E. Group dynamics Flow from the previous talk was maintained Presented material was nto redundant A clear relationship was maintained throughout and a cohesive topic was presented
1. Use of #uorescence to probe An overview the location of aromatic residues 2. Changes in the environment Muraki et al. [6] Fig. 5, Table 3 of active site Trp residues due to mutations and substrate binding 3. pK determination of Glu-35 Inoue et al. [7] Figs. 4, 6 ! via Trp-108 absorbance 4. Determination of dissociaDahlquist et al. [8] Figs. 1, 2 tion constant (derive equation) 5. Circular dichroism: an An overview analysis of secondary structure and analysis of thermostability
order to prepare a clear and concise presentation, students are encouraged to use "gures and an outline format to summarize procedures, results or conclusions. The team is instructed to meet several times so that the members can critique content and clarity of the individual's presentation. Furthermore, such preparation in teams ensures that the #ow between presentations is cohesive and the content not redundant. Journal club articles are organized into the following categories: (1) substrate-binding and mechanism; (2) spectroscopic techniques, including #uorescence and circular dichroism; (3) nuclear magnetic resonance; (4) X-ray crystallography; (5) stability analysis by thermal denaturation. An example of one of these topics, spectroscopy, and the papers selected to illustrate its uses, is given in Table 1. An outline of the criteria for evaluation of the oral presentation is given in Table 2. Since we adopted the supplementary journal club, the quality of research proposals has improved tremendously. Students are able to understand the principles of a variety of physical and chemical techniques for characterization of proteins, and utilize these in preparing their proposals. The research proposal includes the following sections adapted from granting-agency guideliness: summary, prior results, project description, and references. The proposal itself and the peer review process have been described [1]. We have modi"ed the peer review form to provide more guidance to the student reviewers, specifying the desired level of detail, appropriate audience level, requirements for tables and "gures, etc. The guidelines for the project description, which is the core of the proposal, are given in Table 3. Evaluation sheets such as those used for oral presentation and peer review clarify expectations and improve the quality of both the work and the review process.
Table 3 Peer review form for evaluation of research proposal (research project only) Peer evaluation of the xrst draft Directions: For each entry indicate: a. Yes, if this item has been completely addressed b. No, if this item must be corrected, then indicated on what page(s) you have placed the relevant comments c. Additional comments should be made on the reverse side of the form Project description YES/NO (comments on page}}}) 1. Opening statements: are concise are not redundant with the summary 2. Methods to be employed: are presented in a logical order are relevant to the purpose of the study explore all the possible outcomes of the mutation are su$ciently described to understand key steps in the procedure are not as detailed as a Methods section are explained at a level appropriate for scienti"c peers are appropriately referenced 3. Previous studies are mentioned: to support the use of the methods to predict possible outcomes are interpreted as possible outcomes and not certain outcomes are relevant and not just space "ller 4. The information from multiple sources does not dominate the discussion. Estimate the percentage of text dedicated to their proposed work vs. previous studies (65}75% for the proposed work is desirable.) 5. The concluding paragraph: "nishes with a strong summary of your study's goals suggests future work
M.L. Hall, A.J. Wolfson / Biochemical Education 28 (2000) 71}73
3. Conclusions Journal clubs are a familiar format for most scientists, but they are not often seen by undergraduate students. One of the great bene"ts of this exercise is that students are responsible for their own learning; they are provided with a starting place but must work to understand the topic and "nd the best ways to present it to their peers. We have found it to be very successful for a course with an emphasis on methods, but it may be easily adapted to many advanced undergraduate courses.
References [1] A.J. Wolfson, M.L. Hall, T.R. Branham, An integrated biochemistry laboratory, including molecular modeling, J. Chem. Edu. 73 (1996) 1026}1029.
73
[2] T.E. Creighton, Proteins: A Practical Approach, Oxford Press, New York, 1989. [3] I.D. Campbell, R.A. Dwek, Biological Spectroscopy, Benjamin/Cummings, Menlo Park CA, 1984. [4] R.A. Bradshaw, M. Purton, Proteins: Form and Function, Cambridge University Press, New York, 1990. [5] Branden, J. Tooze, Introduction to Protein Structure, Garland Publishing, New York, 1991. [6] M. Muraki, K. Harata, Y. Jigami, Dissection of the functional role of structural elements of tyrosine-63 in the catalytic action of human lysozyme, Biochemistry 31 (1992) 9212}9219. [7] M. Inoue, H. Yamada, Yasukochi, R. Kuroki, T. Miki, T. Horiuchi, T. Imoto, Multiple role of hydrophobicity of tryptophan-108 in chicken lysozyme: Structural stability, saccharide binding ability, and abnormal pK of glutamic acid-35, Biochemistry 31 (1992) ! 5545}5553. [8] F.W. Dahlquist, L. Jao, M. Raftery, On the binding of chitin oligosaccharides to lysozyme, Proc. Nat. Acad. Sci. (USA) 56 (1966) 26}29.