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Illinois Math and Science Academy DigitalCommons@IMSA Posters: Protein Folding & Structure Prediction Examples of Student Work Fall 2015 Poster 2: Primary Structure Max Shramuk '16 Illinois Mathematics and Science Academy Mara Cardona '16 Illinois Mathematics and Science Academy Follow this and additional works at: http://digitalcommons.imsa.edu/protein_folding Part of the Biology Commons, and the Science and Mathematics Education Commons Recommended Citation Shramuk, M., & Cardona, M. (2015). Poster 2: Primary Structure. Retrieved from: http://digitalcommons.imsa.edu/protein_folding/1 This Book is brought to you for free and open access by the Examples of Student Work at DigitalCommons@IMSA. It has been accepted for inclusion in Posters: Protein Folding & Structure Prediction by an authorized administrator of DigitalCommons@IMSA. For more information, please contact [email protected], [email protected]. Primary Structure The peptide chain is written from the N-terminus to the Cterminus. (1) Fig. 2: An example of the difference between cis conformation and trans conformation in an amino acid. Cis means the alpha carbon is on the same side as that of an adjacent amino acid while trans means that alpha carbon is on the opposite side. Picture: (5) Internal carbons tend to be in the trans conformation. (1) Bibliography: 1) Berg, J. M., Tymoczko, J. L., Stryer, L. (2002). Primary Structure: Amino Acids are Linked by Peptide Bonds to Form Polypeptide Chains. Biochemistry (5th ed.). New York: W.H. Freeman. Retrieved from http://www.ncbi.nlm.nih.gov/books/NBK22364/ 2) Breda, A., Valadares, N. F., de Souza, O.N., & Garratt, R.C. (2008). Protein Structure, Modelling, and Applications. Bioinformatics in Tropical Disease Research: A Practical and Case-Study Approach. US: National Center for Biotechnology Information. Retrieved from http://www.ncbi.nlm.nih.gov/books/NBK6824/ 3) Mehta, Sweety. (2013). [Diagram.] Retrieved from: http://pharmaxchange.info/press/2013/10/oxidation-of-odd-carbon-chain-length-fattyacids/. Fig. 1: The general 3D structure of the primary structure of a protein. Note that not everything is in the same plane. Also note the torsion angles; the measurements of these angles will vary between -180 degrees and 180 degrees depending on the R group. (1) However, it will never go to a conformation that is geometrically impossible in the secondary structure. (1) Picture: (3) The peptide bonds are resonance bonds, which are stronger than single bonds but weaker than double bonds. This results in the whole structure being slightly more rigid, but not too rigid. (2) 4) Stoker, H. S. (2015). Amino Acids: The Building Blocks for Proteins. General, Organic, and Biological Chemistry. Boston: Cengage Learning. Retrieved from https://books.google.com/books?id=IBGdBQAAQBAJ&dq=categories+of+amino+acid +side+chains+polar+nonpolar&source=gbs_navlinks_s 5) Trans arrangement of the alpha Cs. [Diagram], Retrieved from: http://biowiki.ucdavis.edu/Biochemistry/Proteins/Protein_Conformation Background image: [Untitled diagram of the 2D structure of the primary structure of a protein.] Retrieved from http://www.genome.gov/Pages/Hyperion/DIR/VIP/Glossary/Illustration/ amino_acid.cfm?key=amino%20acids Max Shramuk and Mara Cardona The R group and lone hydrogen are in a different plane than the Amino Group, thealpha carbon, ahd the carboxyl group. (2) Kinds of Amino Acids (4) Nonpolar Glycine Alanine Valine Polar and neutral Serine Cysteine Tyrosine Polar and acidic Glutamic Acid Aspartic Acid Polar and basic Histidine Lysine Leucine Isoleucine Phenylalanine Asparagine Glutamine Threonine Proline Methionine Tryptophan Arginine Terminal carbons, the carbons that end a peptide chain, are in the cis conformation. (1) The alpha carbon, Amino group, and carboxyl group are planar. Adjacent alpha carbonx between amino acids are also planar. (2) This is the alpha carbon, meaning it’s the carbon off of which the R group is bound.