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Organic Chemistry
6th Edition
Paula Yurkanis Bruice
Chapter 23
The Organic
Chemistry of
Amino Acids,
Peptides,
and Proteins
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Peptides and proteins are polymers of amino acids linked
together by amide bonds:
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Classification of Amino Acids
• Hydrophobic: water-fearing, nonpolar side
chains
– Alkyl side chain
• Hydrophilic: water-loving side chains
– Polar, neutral side chains
– Anionic
– Cationic
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Nonpolar
Side Chains
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Polar,
Neutral
Side
Chains
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Polar, Acidic Side Chains
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Basic, Polar Side Chains
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Configuration of Amino Acids
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Acid–Base Properties of Amino Acids
An amino acid can never exist as an
uncharged compound
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Some amino acids have ionizable hydrogens on their
side chains:
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The isoelectric point (pI) of an amino acid is the pH at
which it has no net charge:
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The pI of an amino acid that has an ionizable side chain
is the average of the pKa values of ionized groups of
the same charge:
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A mixture of amino acids can be separated by
electrophoresis on the basis of their pI values:
Ninhydrin is used to detect the individual amino acids
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A mixture of amino acids can also be separated on the
basis of polarity:
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Ion-exchange chromatography can be used to perform
preparative separation of amino acids:
Negatively charged resin binds selectively to
positively charged amino acids
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Ion-Exchange Chromatography
• Cations bind most strongly to cation-exchange
resins.
• Anions bind most strongly to anion-exchange
resins.
• An amino acid analyzer is an instrument that automates
ion-exchange chromatography.
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Synthesis of Amino Acids
HVZ reaction followed by reaction with ammonia:
Reductive amination:
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A more efficient way of synthesizing amino acids:
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The Strecker Synthesis
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Resolution of Racemic Mixtures of Amino Acids
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Formation of a Peptide
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A peptide bond has 40% double-bond character:
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Formation of Disulfide Bonds
Disulfides can be reduced to thiols
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The disulfide bridge in proteins contributes to the overall
shape of a protein:
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Peptide Examples
ENKEPHALINS
Natural ligands for opioid receptors
Tyr-Gly-Gly-Phe-Leu
Tyr-Gly-Gly-Phe-Met
NUTRASWEET
Peptide-based sweetener
GLUTATHIONE
Antioxidant and
electrophile trap
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Because amino acids have two functional groups,
amide bond formation with a mixture of two amino
acids affords four products:
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Strategy for Making a Specific Peptide Bond
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t-BOC protection of an amine group:
The t-BOC protecting group is stable during amide
bond formation but is removed under acidic conditions
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Carboxylic acid activation by DCC:
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Amide bond formation:
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Amino acids can be added to the growing C-terminal end
by repeating these two steps:
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When the desired number of amino acids has been
added to the chain, the protecting group can be
removed:
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An Improved Peptide Synthesis Strategy
C-terminal amino acid
Attachment of Nprotected amino
acid to resin
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Removal of t-BOC protecting group
Carboxylic acid activation of second amino acid
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Amide bond formation
Removal of t-BOC protecting group
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Carboxylic acid activation of N-terminal amino acid
Amide
bond
formation
Removal of t-BOC protecting group
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Release of tripeptide from
Merrifield resin
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Sequencing Proteins
• N-terminal amino acid?
• C-terminal amino acid?
• What is in between?
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The first step in determining the sequence of amino acids
in a peptide or protein is to cleave the disulfide bridges:
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The next step is to determine the number and kinds
of amino acids in the peptide or protein by hydrolysis
and then analysis of the mixture:
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The N-terminal amino acid of a peptide or a protein can
be determined by Edman degradation:
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The particular PTH–amino acid can be identified by
chromatography using known standards
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The C-terminal amino acid can be identified by treating
the protein with carboxypeptidase:
• Carboxypeptidase B:
ONLY Arg and Lys
• Carboxypeptidase A: ALL
amino acids EXCEPT Arg
and Lys
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The peptide or protein can be partially hydrolyzed using
endopeptidases:
•
•
•
•
Trypsin: C-side of Arg and Lys
Chymotrypsin: C-side of Phe, Tyr, Trp
Elastase: C-side of Gly and Ala
No cleavage for any endopeptidase if Pro on either side
Example of trypsin hydrolysis:
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Cyanogen bromide causes the hydrolysis of the amide
bond on the C-side of a methionine residue:
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Mechanism for cleavage of a peptide bond by
cyanogen bromide:
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Secondary Structure of Proteins
Describes the repetitive conformations assumed by
segments of the backbone of a peptide or protein
Three factors determine the choice of secondary
structure:
• The regional planarity about each peptide bond
• Maximization of the number of peptide groups that
engage in hydrogen bonding
• Adequate separation between nearby R groups
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The a-helix is stabilized by hydrogen bonds:
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Not all amino acids are able to fit into an a-helix:
• Prolines distort the helix.
• Two adjacent Val, Ile, or Thr cannot fit into a helix.
• Two adjacent residues with the same charges cannot
fit into a helix.
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Two Types of b-Pleated Sheets
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Most globular proteins have coil or loop conformations:
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The tertiary structure is the three-dimensional
arrangement of all the atoms in the protein:
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The tertiary structure is defined by the primary structure
The stabilizing interactions include covalent bonds,
hydrogen bonds, electrostatic attractions, and
hydrophobic interactions
Disulfide bonds are the only covalent bonds that can
form when a protein folds
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Quaternary Structure of Proteins
Proteins that have more than one polypeptide chain are
called oligomers
The individual chains are called subunits
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