Amino Acids & Proteins

Skip: 24-7C; 24-12:24-14
1. Structure of Twenty -amino acids (Table 24-2)
2. Acid/Base properties (Section 24-3)
a. Zwitterions
b. pKa’s
c. Isoelectric Point: pH of Neutral zwitterion (Section 24-4)
d. Gel electrophoresis
o Buffered solution selects for particular charge state depending on
isoelectric point
o high charge density elutes first
3. Synthesis of Amino Acids (Summary p 1168)
a. Reductive Amination of -ketoacid (RCOCOOH to RCHNH2COOH)
b. SN2 reaction of ammonia (excess) with -haloacid (24-5B)
c. Gabriel-Malonic Ester Synthesis (Section 24-5C)
o N-phthalimidomalonic ester alkylation with NaOEt then RX
o Hydrolysis of ester and release of N
o Decarboxylation with heat
d. The Strecker Synthesis: RCHO + NH3 and HCN then H3O+: (Mechanism
pg 1168)
o Formation of Imine
o Formation of -amino propionitrile
o Hydrolysis of nitrile to carboxylic acid
4. Amino Acid Reactivity (review)
a. Acylation of amino group
b. Esterification of Carboxylic Acid group
5. Resolution of Amino Acids (Section 24-6)
a. React racemic aa with acetic anhydride
b. expose to enzymatic deacylation with an “acylase” enzyme to hydrolyse
selectively just the natural (L) amino acid
6. Peptides (Section 24-8)
7. The peptide bond: Amide between amino acids
a. Naming convention: N terminus at left; C terminus at right
b. Primary structure: Three letter designations (Arg-Pro-Gly)
8. Sequencing : Determining the Amino Acid Composition of a polypeptide (Section
a. Disulfide Linkage cleavage
b. Acid-catalyzed Hydrolysis
c. Trypsin Cleavage: C-terminus of basic amino acids lysine& arginine
d. Chymotrypsin cleavage: C-terminus of aromatic aa Phe, Tyr, Trp
9. Edman Degradation: Grabbing the N-Terminus (Section 24-9C)
a. Rxn with phenyl isothiocyanate (S=C=N-Ph) to bind to N-terminus
b. Acid catalyzed Intramolecular rxn with C=O of same amino acid
c. Decomposition of thiazolinone to expel N-terminus aa
10. Peptide Synthesis (aa1-aa2)
a. Traditional solution synthesis (Section 24-10B)
o Protect N-terminus of aa1 with benzylchloroformate
(PhCH2OCOCl) to make Z-aa1
o Activate C-terminus of aa1 with ClCOOEt ethylchloroformate
o Join together with aa2 protected at C terminus as ester
o Remove benzyl protecting group with hydrogenation H2/Pd to
make aa1-aa2(ester)
b. Merrifield Solid Phase synthesis (Section 24-11B)
o Protect N-terminus with BOC anhydride (Me3COOCOOEt)
o Bond carboxylate of aa2 to solid support via SN2 at bonded
Benzyl chloride branches
o Remove N-protection w CF3COOH (release CO2 and
o Couple to second aa with DCC (dicyclohexylcarbodiimide)
o Rinse solid support to remove by-products like CH2=CMe2
o Add second N-protected amino acid via C-terminus
 Identify amino acids.
 Identify the structure of a specific amino acid at a given pH
 Understand the role of protecting groups in Organic synthesis
 Propose a series of reactions to produce a given polypeptide.
 Propose a sequence of steps to sequence a polypeptide using traditional wet chemistry
and using solid support Merrifield Synthesis.
 Given evidence from the results of a polypeptide sequencing experiment, deduce the
primary structure of a polypeptide.
 Draw the mechanism for Edman degradation of a peptide using curved arrow
 Propose an appropriate laboratory method(s) for the separation and identification of a
1. Draw the fragments that would form if the following polypeptide were treated with
2. Draw the structure of the amino acid cysteine at pH 8.
3. A heptapeptide contains the amino acids arginine, glycine, isoleucine, phenylalanine,
proline (two residues) and valine.
Treatment of the heptapeptide with trypsin gives arginine and a hepeptide.
Some of the fragments that were obtained by partial hydrolyses of the heptapeptide
are Pro-Phe-Ile, Arg-Gly-Pro, Pro-Phe-Ile-Val and Pro-Pro.
Assign a structure to the heptapeptide.
4. Draw the organic products A, B and C missing from the following reaction sequence.
Include stereochemistry where appropriate: