22.6. How Do Amino Acids Combine to Form Proteins?, 587
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Exploding Soap Bubbles: Hydrogen + Oxygen A series of three videos shows that as the ratio of oxygen to hydrogen in soap bubbles increases, the explosions that occur when the bubbles are ignited get louder. (The fact that with an excess of oxygen the explosions would become softer again is not shown.) Each video is repeated with no voice-over so that only the sounds of the explosions are heard. Five still images are provided to show the stoichiometry on the molecular scale. The videos are intended to be shown in order beginning with Hydrogen Alone and ending with hydrogen plus more oxygen.
Stoichiometry : LimitingReagent (8 Variations) The synthesis of urea by Frederich W??hler in 1825 began the decline of the idea that "organic" chemicals could only be made by living organisms as part of their biological processes.
AgOCN(aq) + NH4Cl(aq)AgCl(s) + NH2CONH2(aq)
If you perform this reaction and collect the following table of data, in which trial(s) is AgOCN clearly the limiting reactant?
Trial
AgOCN used
NH4Cl
AgCl produced
1
20.4 mL
5.3 mL
2.4 g
2
20.3 mL
10.4 mL
4.3 g
3
20.6 mL
15.4 mL
6.2 g
4
20.5 mL
20.6 mL
8.2 g
5
20.4 mL
25.2 mL
10.2 g
6
20.3 mL
30.4 mL
10.3 g
The mL of AgOCN and NH4Cl are the initial amounts used, the mass of AgCl is how much was recovered from the reaction. (Hint: You do not need to do any calculations to answer this question.)
Nature's Way To Make the LantibioticsHeather A. Relyea and Wilfred A. van der Donk This article focuses on one class of antimicrobial compounds, the lantibiotics, and discusses their biosynthetic pathways as well as their molecular mode of action. In the course of the review, the meaning of the terms regio-, chemo-, and stereoselectivity are discussed. Relyea, Heather A.; van der Donk, Wilfred A. J. Chem. Educ.2006, 83, 1769.
Applications of Chemistry |
Bioorganic Chemistry |
Biotechnology |
Biosynthesis |
Catalysis |
Drugs / Pharmaceuticals |
Proteins / Peptides
Gifts from Mother Earth—The Good, the Bad, and the UglySabine Heinhorst and Gordon C. Cannon Recent articles from the journal Nature that deal with good, bad, and ugly gifts from Mother Earth are described. Heinhorst, Sabine; Cannon, Gordon C. J. Chem. Educ.2006, 83, 196.
Biosynthesis |
Biotechnology |
Natural Products |
Nutrition |
Plant Chemistry |
Polymerization |
Proteins / Peptides
A Green Polymerization of Aspartic Acid for the Undergraduate Organic LaboratoryGeorge D. Bennett Based on a technology that won a Presidential Green Chemistry Challenge Award, this experiment involves the thermal polymerization of aspartic acid and subsequent hydrolysis to give sodium poly(aspartate). The procedure is suitable for introducing students to the important topic of polymers and for illustrating several of the principles of green chemistry. Bennett, George D. J. Chem. Educ.2005, 82, 1380.
Molecular Model of Creatine SynthesisWilliam F. Coleman The featured molecules for this month come from the paper Creatine Synthesis: An Undergraduate Organic Chemistry Laboratory Experiment by Andri Smith and Paula Tan on the synthesis of creatine in introductory organic chemistry. This synthesis is sufficiently straightforward to be used in non-majors and general chemistry courses. The structures illustrate some of the limitations associated with the computation of molecular structure. The two adenosine phosphates ADP and ATP exhibit a large number of conformations due to rotation of the adenine system around the bond to the ribose ring, multiple rotational conformations in the phosphate groups, the ionic state of the compound, and the interaction with the solvent or another species such as creatine. The structures that are given for ADP and ATP are derived from PM3MM calculations and are very similar to those derived using the UFF force field. Sarcosine, creatine, and creatine phosphate were treated using the model chemistry B3LYP/6-31+G(d). Perhaps the most interesting structural feature is found in the small molecule cyanamide. Observant students might notice in the Web-based structure that the NCN grouping in cyanamide is non-linear, with an angle of about 177°. This is found for essentially all levels of theory we examined up through the G2 combined model. For students who do notice this deviation from linearity it is useful to ask them whether they are surprised, ask them to defend their answer, send them to the literature to see whether such behavior is seen for cyanamide in other phases (it is), and finally to speculate on possible explanations for the observed non-linearity.
Molecular Modeling |
Molecular Properties / Structure
Parallel Combinatorial Synthesis of Azo DyesWilliam F. Coleman The featured molecules for this month are from "Parallel Combinatorial Synthesis of Azo Dyes: A Combinatorial Experiment Suitable for Undergraduate Laboratories" by Benjamin W. Gung and Richard T. Taylor. The principle of combinatorial chemistry is illustrated by generating a relatively large number of colorful dyes using only one common reaction, the diazo coupling, and two common reactants with small variations. Fully manipulable (Chime) versions of these molecules appear below.
Molecular Modeling |
Molecular Properties / Structure
Bioorganic Synthesis; Monosodium Glutamate and Other Amino AcidsWilliam F. Coleman The March featured molecules are discussed in the article "The Monosodium Glutamate Story: The Commercial Production of MSG and Other Amino Acids". This paper provides a number of opportunities for introducing students to the importance of stereochemistry in bioorganic synthesis. The collection here includes all of the relevant molecules in the synthesis of α-amino-ε-aminocaprolactam (ACL). The introduction of two chiral centers in the reaction of cyclohexene with NOCl results in four diastereomers, and it is instructive to ask students to predict the relative abundance of those isomers and the dependence of that distribution on the extent to which the reaction is syn- or anti-addition, and to account for the fact that the resultant oxime, and the ACL, are obtained as racemates.
AgCl(s) + NH2CONH2(aq) 
Go for the oxidation of 2 mole of silver in the following balanced reaction. 
Ca(s) + 2AgI(s) 
