In the Classroom
Prote-ACE A Logic Puzzle To Determine a Polypeptide Sequence Craig P. McClure Department of Chemistry, The University of Alabama at Birmingham, Birmingham, AL 35294-1240;
[email protected] Chemistry is a logical pursuit and frequently requires a combination of orthogonal data sets to solve a problem. An example of this would be using multiple spectral techniques or a spectrum combined with other data to elucidate a chemical structure. Popular culture frequently ignores this necessity for combining multiple data sets, as can be seen with a “one instrument, one button” approach to determining the identity of a chemical compound or mixture of compounds that is portrayed on television shows such as CSI: Crime Scene Investigation. Puzzles have previously been published in this Journal that require a logical approach to combining information to solve a chemical problem (1–3). These puzzles also reinforce important concepts that are introduced in a course and emphasize the logical nature of chemical research. The logic puzzle shown here deals with determination of the amino acid sequence of a peptide and requires a knowledge of characteristics and structure of amino acid side chains, differentiation of amine and carboxyl termini of a peptide, and terminology used to describe peptides. Proteases are also discussed, and the characteristic cleavage patterns of each are necessary information for determination of the amino acid sequence (4–7). This puzzle is appropriate for application of these concepts in a biochemistry course. Are You a Prote-ACE? Proteases are enzymes that break down proteins into smaller peptides by hydrolyzing peptide bonds. Some proteases are nonspecific and will hydrolyze peptide bonds with little selectivity for the amino acids present, while some are much more selective about which bonds will be broken in a protein. Some proteases and chemicals that break specific bonds are
• Chymotrypsin – cuts on the C-terminal side of tyrosine, phenylalanine, and tryptophan
• Trypsin – cuts on the C-terminal side of lysine and arginine
• Thermolysin – cuts on the N-terminal side of leucine, phenylalanine, isoleucine, and valine
• Pepsin – cuts on the C-terminal side of phenylalanine, leucine, and glutamic acid
• Cyanogen bromide – cuts on the C-terminal side of methionine
An octapeptide made up of 8 different amino acids was treated (digested) with each of these proteases and cyanogen bromide at biological pH and placed under an electrical potential to determine the charge characteristics. The following information was obtained on each resulting peptide:
• Digestion with pepsin resulted in two tetrapeptides, with no charge on either fragment.
• Digestion with trypsin resulted in a negatively-charged tripeptide and a positively-charged pentapeptide.
• Digestion with chymotrypsin resulted in a tripeptide and pentapeptide, both with no overall charge.
• Treatment with cyanogen bromide yielded only the octapeptide, with no overall charge
• Digestion with thermolysin resulted in a positively-charged tripeptide, a neutral tripeptide, and a negatively-charged dipeptide.
Additionally, the following information is obtained:
• Only one amino acid contains a sulfur atom, and it is closer to N-terminus than the C-terminus
• Only one amino acid has two carbons in its side chain (the α-carbon is not included in this count)
• The second amino acid from the N-terminus does not contain a chiral carbon
• Only one amino acid side chain contains a heterocyclic amine
• Glutamine is adjacent to one amino acid with a charged side chain
• Two amino acids have four carbons in their side chains
• There are 2 amino acids between valine and the nearest amino acid with a nonpolar side chain
• Only one amino acid has multiple nitrogen atoms in its side chain
With the information stated above, determine the order of amino acids in the octapeptide (list them in order from Nterminus to C-terminus; solution given below). Literature Cited 1. Boyd, Susan L. J. Chem. Educ. 2007, 84, 619–621. 2. Castro-Acuna, Carlos M.; Dominguez-Danache, Ramiro E.; Kelter, Paul B.; Grundman, Julie. J. Chem. Educ. 1999, 76, 496–498. 3. Peris, Miguel. J. Chem. Educ. 2007, 84, 609–609. 4. Bark, Steven J.; Muster, Nemone; Yates, John R.; Siuzdak, Gary. J. Am. Chem. Soc. 2001, 123, 1774–1775. 5. Keil, Borivoj. Specificity of Proteolysis; Springer-Verlag: New York, 1992; p 11. 6. Konigsberg, William; Hill, Robert J.; Goldstein, Jack. J. Biol. Chem. 1963, 238, 2028–2033. 7. Lill, Ute; Schreil, Angelika; Henschen, Agnes; Eggerer, Hermann. Eur. J. Biochem. 1984, 143, 205–212.
Supporting JCE Online Material
http://www.jce.divched.org/Journal/Issues/2009/Apr/abs457.html Abstract and keywords Full text (PDF) Links to cited JCE articles Supplement A student-ready version of this activity
Solution: Cys–Gly–Trp–Leu–Arg–Gln–Val–Asp
© Division of Chemical Education • www.JCE.DivCHED.org • Vol. 86 No. 4 April 2009 • Journal of Chemical Education
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