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pH is adjusted so that an amino acid's carboxylate and ammonium ions are at exactly equal concentrations; uncharged overall; isoelectronic point
1. treat a carboxylic acid with P and Bromine, then
2. nucleophilic substitution in which ammonia reacts with an a-halo carboxylic acid to form an amino acid
combines three reactions in two steps: cyanohydrin formation followed by immediate alcohol to amine conversion, then hydrolysis
converts an aldehyde into an amino acid with the amine group on the former carbonyl carbon and a new carbon at the carboxyl position
1. treated with the ethoxide ion to form malonate's enolate ion
2. this is used to displace Cl or Br from an alkyl or benzyl halide
3. aqueous acid hydrolysis removes both the amide group and the ester alkoxy groups, allowing decarboxylation to the amino acid
typical of the amino group; when treated with acid anhydride or acyl chloride, it converts to its amide
typical of carboxyl group; treating the amino acid with the desired alcohol using dry HCl as a catalyst
decarboxylation, transamination, tryosine derivations, enzymatic oxidation and hydrolysis
results from incomplete breakdown of amino acids resulting in oxygenated products of ammonia, which is tied up as urea; lack phenylalanine hydroxylase
removes one amino acid at a time, allowing successive identification of each amino acid from the N-terminus inward; phenyl-N=C=S; C=S acts as an internal nucleophile
used for end-group analysis from the C-terminus; cleave just the C-terminus amino acid, so observation of which amino acids are freed in sequence can indicate the primary structure
vaporizes peptides that lack sufficient volatility to be vaporized for analysis by conventional MS
amino group protection results in? and uses benzyloxycarbonyl (Cbz or Z) and tert-butoxycarbonyl (Boc) and 9-fluorenylmethoxycarbonyl (FMOC) groups
can't use hydrolysis (would hydrolyze amide bonds too)
1. HBr in acetic acid
2. hydrogenolysis in palladium
3. basic conditions, NH3
methyl and ethyl esters are removed by dilute base, while benzyl esters can be removed by hydrogenolysis
reagent used to couple the protected amino acids; yields dicyclohexylurea as it combines with the water released by peptide bond formation
it and its urea are soluble in water and can be easily separated; can be used in organic solvents
solid-phase peptide synthesis
an insoluble polymer support is used as the protecting group for the C-terminus. Boc-protected amino acids are coupled in sequence using DCCI, deptrotected, washed, and then coupled, deptrotected, etc.
once complete, the peptide can by removed by HBr in CF3COOH. THIS CAN BE AUTOMATED
when placed in water, nonpolar amino acid side chains cause water molecules to become more ordered causing the protein to adopt a spherical shape which puts nonpolar inside
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