In the Classroom
Amino Acid Crossword Puzzle Paul A. Sims Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
[email protected] Learning the 20 standard amino acids is an essential component of an introductory course in biochemistry; this knowledge is part of the grammar or vocabulary of biochemistry. Accordingly, amino acids are introduced relatively early in most biochemistry textbooks, and at this time the students learn the names, the structures, the three- and one-letter codes, and the chemical properties (e.g., acid-base chemistry) of the amino acids. Later in the introductory course, the students study
metabolism and learn about various catabolic and anabolic pathways involving amino acids. Learning new material or concepts often is easier if one can connect the new material to what one already knows; thus, the following crossword puzzle1 (Figure 1) aims to connect some of the fundamental properties of the standard amino acids (composition of the side chains) with some of the latter, metabolic properties. Because the metabolic properties in this
Figure 1. Crossword puzzle that connects some fundamental properties of the standard amino acids with some metabolic properties.
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Vol. 88 No. 4 April 2011 pubs.acs.org/jchemeduc r 2011 American Chemical Society and Division of Chemical Education, Inc. 10.1021/ed100780n Published on Web 02/03/2011
In the Classroom
Across 1a) 2a) 3a) 4a) 5a)
side chain is a methyl group side chain has two methylenes then a carboxylate group amide “cousin” to aspartate side chain has a methylene then a carboxylate group side chain consists of a hydroxymethyl group, that is, a primary alcohol
Down 1d) side chain has three methylenes then a guanidino/guanidinium group 2d) side chain has a methylene then phenol group 3d) side chain has two methylenes then an amide group 4d) non-chiral alpha carbon 5d) side chain has a methylene then a thiol 6d) technically an imino acid
Sloping (diagonal) 1s) side chain has four methylenes then a primary amino/ammonium group 2s) side chain has a secondary alcohol 3s) side chain has a methylene then an imidazole ring 4s) side chain has two methylenes, a sulfur, and then a methyl group 5s) side chain is a sec-butyl group 6s) side chain is a benzyl group 7s) side chain has a methylene then an indole ring 8s) side chain is an isobutyl group 9s) side chain is an isopropyl group
Questions 1. What do all of the “across” amino acids have in common? 2. What do all of the “down” amino acids have in common? 3. What do all of the “sloping” amino acids have in common? Figure 2. Diagrams used to help answer the questions.
Hint
example require three different groupings, a “third dimension” was needed in the crossword puzzle; hence, the sloping or diagonal entries. After one fills in the crossword puzzle according to the accompanying clues, one can then try to answer three related questions about the different groupings. Hints are provided in the form of diagrams (Figure 2) as discussed below. The supporting information contains answers to the puzzle and questions, as well as Adobe Illustrator files so that one can modify the puzzle or diagrams to include, for example, pyrollysine, selenocysteine, taurine, or other nonstandard amino acids. Crossword Puzzle Execution For all of the clues shown below, consider the form that predominates at physiological pH. For example, use aspartate instead of aspartic acid.
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One may use the diagrams in Figure 2 to help answer the above questions; these diagrams should be filled-in with the appropriate amino acids such that the encircled letters spell a phrase when read vertically from top to bottom. The phrases provide clues to answer the above questions. A few amino acids have been entered to get one started. Discussion The answers to what the amino acids have in common are (i) not needed; (ii) may need; and (iii) need these. The “not needed” amino acids are the nonessential amino acids. These amino acids are not needed in a nutritional sense because humans can synthesize these amino acids; thus, they do not have to be included in our diet. The “may need” amino acids are the conditionally essential amino acids that are “required to some degree in young, growing animals, or sometimes during illness” (1). The “need these” amino acids are the essential amino
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In the Classroom
acids that we must obtain in our diet because we are unable to synthesize these amino acids. The above categories are often discussed in conjunction with the biosynthetic pathways of the 20 standard amino acids. These discussions generally follow discussions of major metabolic pathways such as glycolysis and the citric acid cycle. This sequence of presentation facilitates learning the amino acid biosynthetic pathways because a number of amino acids are derived from intermediates of glycolysis or the citric acid cycle and thus students are in a position to make connections with this previous information. Acknowledgment I thank Gary O'Mealey, Katie Branscum, Chelsea Larabee, and Vidya Kumar for valuable feedback regarding the puzzle.
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Note 1. Various crosswords, games, puzzles, and wordsearches have been published in this Journal and can be found by searching on the aforementioned terms.
Literature Cited 1. Nelson, D. L.; Cox, M. M. Lehninger Principles of Biochemistry, 5th ed.; W. H. Freeman and Company: New York, 2008; Chapter 18, p 686.
Supporting Information Available Answers to the crossword puzzle and related questions; additional discussion. This material is available via the Internet at http://pubs.acs.org.
Note Added after ASAP Publication This version of this paper that was published on 2/3/2011 was missing a supporting information file. It was added to the version published on 2/11/2011.
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