Biochemistry Online: An Approach Based on Chemical Logic

CHAPTER 2 - PROTEIN STRUCTURE

BIOCHEMISTRY - DR. JAKUBOWSKI

Last Update: 02/27/16

Learning Goals/Objectives for Chapter 2A: After class and this reading, students will be able to

state the charge on amino acid side chains using the Henderson Hasselbach equation and the approximate charge by inspection at any given pH
draw mechanisms and identify products for the reaction of nucleophilic side chains Lys and Cys with common chemical modification agents and extend this understanding to reactions of His.
draw mechanisms for disulfide exchange reactions for sulfhydryls using them and oxidation numbers to explain redox reactions of cysteine/cystine.

reacts with anhydride in a nucleophilic substitution reaction (acylation).
reacts reversibly with methylmaleic anhydride (also called citraconic anhydride) in a nucleophilic substitution reaction.
reacts with high specificity and yield toward ethylacetimidate in a nucleophilic substitution reaction (ethylacetimidate is like ethylacetate only with a imido group replacing the carbonyl oxygen). Ethanol leaves as the amidino group forms. (has two N -i.e. din - attached to the C)

reacts with O-methylisourea in a nucleophilic substitution reaction. with the expulsion of methanol to form a guanidino group (has 3 N attached to C, nidi)
reacts with fluorodintirobenzene (FDNB or Sanger's reagent) or trinitrobenzenesulfonate (TNBS, as we saw with the reaction with phosphatidylethanolamine) in a nucleophilic aromatic substitution reaction to form 2,4-DNP-lysine or TNB-lysine.
reacts with Dimethylaminonapthelenesulfonylchloride (Dansyl Chloride) in a nucleophilic substitution reaction.

reacts with high specificity toward aldehydes to form imines (Schiff bases), which can be reduced with sodium borohydride or cyanoborohydride to form a secondary amine.

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Archived version of full Chapter 2A: Amino Acids