Polyfunctional Natural Products: Carbohydrates

1
Chapter 26
Introduction to Amino Acids and Polyamino Acids
Peptides and Proteins
Page 1343
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Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• Introduction (See Chapter 21 on Amines page 1075)

Biologically important molecules containing
nitrogen! PROTEINS!
3
Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.1 AMINO ACIDS
• 26.1b Nomenclature (page 1344)
• Commonly used nomenclature denoting position of
  amino function ?, ?, ?, or ?.

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Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.1a Nomenclature (page 1344)
• Nomenclature using numbers

Watch out! Systematic names are rarely used.
Some ?-amino acids. Figure 26.2
5
Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.1a Nomenclature (page 1345)
• Biochemist tend to view ?-amino acids as
  R-substituted 2-amino acetic acid.

An ?-amino acid is just an R-substituted
2-amino acetic acid. Figure 26.3
6
Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.1a Nomenclature (page 1345)
• Three and even one letter codes have been
  developed to denote the various natural amino
  acids. Examples

R Common Name Abbreviations H Glycine Gly,
G CH3 Alanine Ala, A CH(CH3)2 Leucine Leu, L
See Table 26.1 for the Names and Properties of
all the 20 Common Natural Amino Acids.
7
Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.1a Nomenclature (page 1345)
• Essential Amino acids

How many different amino acids are encountered in
naturally occurring peptides and proteins?
20
How many do humans lack?
10
8
Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.1a Structure of Amino Acids (page 1345)
• With one exception all natural amino acids are
  primary amines.

Of the 20 common ?-amino acids, only proline is
not a primary amine Figure 26.4
9
Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.1a Structure of Amino Acids (page 1346)
• All biologically important amino acids are
  L-amino acids except achiral Glycine.

An (S) amino acid is L in the Fischer
terminology. Figure 26.5
10
Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.1a Structure of Amino Acids (page 1346)
• All biologically important amino acids are
  L-amino acids except achiral Glycine.

Problem 26.1 Draw tetrahedral three-dimensional
structures for (R) and (S) valine and aspartic
acid.
11
Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.1a Structure of Amino Acids (page 1347)
• All biologically important amino acids are
  L-amino acids except achiral Glycine.

Problem 26.2 Draw L-isomers of valine and
cysteine in Fischer projection.
12
Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.1a Structure of Amino Acids (page 1347)
• All biologically important amino acids are
  L-amino acids except achiral Glycine.

From Table 26.1 can be seen that amino acids are
high-melting solids. Why?
13
Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.1c Acid-Base properties of Amino Acids (page
  1348)

What happens here?
What reaction must occur between these two
molecules Figure 26.6
14
Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.1c Acid-Base properties of Amino Acids (page
  1348)

An amine and a carbonxylic acid must undergo
acid-base chemistry to give an ammonium salt of
the acid. Figure 26.7
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Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.1c Acid-Base properties of Amino Acids (page
  1348)

Ionic compounds!
In amino acids, an intramolecular version of the
same reaction gives a zwitterion. Figure
26.7
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Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.1c Acid-Base properties of Amino Acids (page
  1348)
• Amino acids have two (or more) pKa values.

Explain
At low pH, the zwitterion will protonate to give
a net positively charged ion. At high pH, a
carboxylate anion, net negatively charged, will
be formed. Figure 26.7
17
Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.1c Acid-Base properties of Amino Acids (page
  1349)
• Amino acids have two (or more) pKa values.

At low pH, the zwitterion will protonate to give
a net positively charged ion. At high pH, a
carboxylate anion, net negatively charged, will
be formed. Figure 26.7
18
Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.1c Acid-Base properties of Amino Acids (page
  1349)
• Amino acids have two (or more) pKa values.

Problem 26.3 The pKa for a simple organic acid
is 4-5. Why are amino acids so much more acidic?
19
Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.1c Acid-Base properties of Amino Acids (page
  1349)
• Amino acids have two (or more) pKa values.

20
Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.1c Acid-Base properties of Amino Acids (page
  1349)
• Amino acids have two (or more) pKa values.
• A more complicated case!

Arginine is twice protonated at low pH. Figure
26.9
21
Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.1c Acid-Base properties of Amino Acids (page
  1350)
• Amino acids have two (or more) pKa values.
• A more complicated case!

Problem 26.5 In the guanidino group of arginine,
where is the side of initial protonation?
22
Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.1c Acid-Base properties of Amino Acids (page
  1350)
• Amino acids have two (or more) pKa values.
• A more complicated case!

Problem 26.6 Why is the five-membered ring (an
imidazole) in histidine so acidic (Table 26.1)?
23
Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.1c Acid-Base properties of Amino Acids (page
  1350)
• Amino acids have two (or more) pKa values.
• Electrophoresis, a powerful technique to separate
  amino acids based on the differences in
  isoelectric points.

The charge states of Lys, Phe and Glu at pH
5.5. Figure 26.10
24
Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.1c Acid-Base properties of Amino Acids (page
  1350)
• Amino acids have two (or more) pKa values.
• Electrophoresis, a powerful technique to separate
  amino acids based on the differences in
  isoelectric points.

Separation of three amino acids by
electrophoresis Figure 26.11
25
Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.1d Syntheses of Amino Acids (page 1351)
• A simple approach!

Simple alkylation of an ?-halo acid will give an
?-amino acid. Figure 26.9
26
Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.1d Syntheses of Amino Acids (page 1351)
• A simple approach!

Simple alkylation of an ?-halo acid will give an
?-amino acid. Figure 26.9
27
Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.1d Syntheses of Amino Acids (page 1351)
• A simple approach!

Problem 26.7 Devise simple syntheses of the
following ?-bromo acids starting from alcohols
containing no more than four carbon atoms and
inorganic reagents of your choice (Fig. 26.13)
(see Section 19.6b, p. 987).
28
Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.1d Syntheses of Amino Acids (page 1352)
• Another application of the Gabriel synthesis the
  Gabriel malonic ester synthesis.

29
Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.1d Syntheses of Amino Acids (page 1352)
• Gabriel malonic ester synthesis

Problem 26.9 Provide detailed mechanisms for the
reactions at the bottom of Figure 26.14.
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Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.1d Syntheses of Amino Acids (page 1352)
• Gabriel malonic ester synthesis

Problem 26.10 In a simpler version of this
reaction, acetamidomalonic ester is used (Fig.
26.15). Sketch out the steps in this related
amino acid synthesis.
31
Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.1d Syntheses of Amino Acids (page 1353)
• The Strecker Synthesis

What happens here?
The Strecker amino acid synthesis Figure 26.16
32
Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.1d Syntheses of Amino Acids (page 1353)
• The Strecker Synthesis

The Strecker amino acid synthesis Figure 26.16
33
Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.1d Syntheses of Amino Acids (page 1353)
• The Strecker Synthesis

The Strecker amino acid synthesis Figure 26.16
34
Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.1d Syntheses of Amino Acids (page 1353)
• The mechanism of the Strecker Synthesis

The mechanism of the Strecker amino acid
synthesis Figure 26.16
35
Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.1e Resolution of Amino Acids (page 1354)

All syntheses mentioned sofar lead to racemic
amino acids. Devise a method for obtaining the
amino acids as pure enantiomers.
Transformation in a pair of diastereomers
Diastereomeric Ammonium Salts
36
Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.1e Resolution of Amino Acids (page 1355)

Figure 26.18 (page 1355)
37
Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.1e Resolution of Amino Acids (page 1354)
• Enantioselective synthesis of amino acids by
  nature!

Enzymatic reductive amination of ?-ketoglutaric
acid to L-Glutamic acid.
Synthesis of an optically active L-amino acid
through reductive amination. Figure 26.19
38
Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.1e Resolution of Amino Acids (page 1354)
• Enantioselective synthesis of amino acids by
  nature!

Enzymatic reductive amination of ?-ketoglutaric
acid to L-Glutamic acid.
Write out the various steps of this process. What
is the function of the enzyme?
Synthesis of an optically active L-amino acid
through reductive amination. Figure 26.19
39
Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.1e Resolution of Amino Acids (page 1354)
• Enantioselective synthesis of amino acids by
  nature! NAD structure (Chapter 16, 802)

Nicotinamide adenine dinucleotide, NAD Figure
16.90
40
Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)
Chapter 16, page 803
Nicotinamide adenine dinucleotide, NAD Figure
16.90
The NAD is reduced by transfer of hydride (H-)
from ethyl alcohol. Figure 16.91
41
Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.1e Resolution of Amino Acids (page 1354)
• Enantioselective synthesis of amino acids by
  nature!

How do enzymes accomplish an enantioselective
synthesis?
42
Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.1e Resolution of Amino Acids (page 1356)
• Enantioselective synthesis of amino acids using
  nature.

• Fermentation using microorganisms produces
  L-amino acids.
• The use of enzymes to achieve kinetic resolution!
  A biomimetic method.

43
Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)
A kinetic resolution of a pair of enantiomeric
amino acids. Figure 26.20
44
Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.2 REACTIONS OF AMINO ACIDS (page 1356)
• 26.2a Acylation Reactions (page 1357)

Problem 26.12 Write a mechanism for the
acylation reactions of Figure 26.21
The amino group of an amino acid can be
acylated. Figure 26.21
45
Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.2 REACTIONS OF AMINO ACIDS (page 1356)
• 26.2b Esterification Reactions (page 1357)

Problem 26.13 If amino acids are typically in
their zwitterionic forms, how are acylation and
esterification reactions, which depend on the
presence of free amine or acid groups, possible.
Fischer esterification of the acid group of an
amino acid. Figure 26.21
46
Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.2 REACTIONS OF AMINO ACIDS (page 1356)
• 26.2b Reaction with Ninhydrin (page 1357)

Ninhydrine is used to detect amino acids. It
forms the same purple molecule with all amino
acids.
Problem 26.14 Why is the trione hydrated at the
middle, bot the side carbonyl group?
Ninhydrin is the hydrate of indan-1,2,3-trione.
Figure 26.23
47
Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.2 REACTIONS OF AMINO ACIDS (page 1356)
• 26.2b Reaction with Ninhydrin (page 1357)

Ninhydrine is used to detect amino acids. It
forms the same purple molecule with all amino
acids.
How can this be?
Fischer esterification of the acid group of an
amino acid. Figure 26.21
48
Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.2 REACTIONS OF AMINO ACIDS (page 1356)
• 26.2b Reaction with Ninhydrin (page 1357)

49
Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.3 PEPTIDE CHEMISTRY (page 1359)
• Polymerization to Peptides en Proteins

Polypeptides are polyamino acids linked through
amide bonds. Figure 26.25
50
Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.3 PEPTIDE CHEMISTRY (page 1359)
• 26.3a Nomenclature and Structure

The tripeptide, alanylserinylvaline, Ala-Ser-Val.
The amino acid terminus starts the name, and the
carboxy terminus ends it. Figure 26.26
51
Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.3 PEPTIDE CHEMISTRY (page 1359)
• 26.3a Nomenclature and Structure

The tripeptide, alanylserinylvaline, Ala-Ser-Val.
The amino acid terminus starts the name, and the
carboxy terminus ends it. Figure 26.26
52
Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.3 PEPTIDE CHEMISTRY (page 1360)
• 26.3a Nomenclature and Structure

Problem 26.15 Write structures for the peptides
named in the yellow box in Figure 26.27.
Problem 26.16 Name the peptides drawn in Figure
26.27.
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Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.3 PEPTIDE CHEMISTRY (page 1360)
• 26.3a Nomenclature and Structure

• Primary structures of peptides and proteins are
  made up by the sequence of amino acids and
  possible connections between chains

Formation of disulfide bonds can link one
polyamino acid chain to another. Figure
26.28
54
Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.3 PEPTIDE CHEMISTRY (page 1360)
• 26.3a Nomenclature and Structure

• The secondary structures or folding pattern of
  peptides and proteins are made up by
• Planarity of the amide function.
• Internal hydrogen bonds between NH hydrogens and
  carboxy carbonyl groups

Problem 26.17 Explain carefully why amides
prefer planarity.
55
Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.3 PEPTIDE CHEMISTRY (page 1361)
• 26.3a Nomenclature and Structure

• Coils
• ?-helical
• random

? -Pleated sheets
Two examples of ordered secondary structure of
polypeptides, the ?-helix and the ?-pleated
sheet. Figure 26.29
56
Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.3 PEPTIDE CHEMISTRY (page 1362)
• 26.3a Nomenclature and Structure

• The tertiary structures of peptides and proteins
  are made up by
• Hydrogen bonding
• Van de Waals forces and electrostatic interactions

Basic overall structure of Proteins A carbon
backbone with side chains/groups Polar
hydrophilic groups Apolar hydrophobic groups
57
Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.3 PEPTIDE CHEMISTRY (page 1362)
• 26.3a Nomenclature and Structure

Tertiary structure!
A globular protein, ordered so as to put the
nonpolar side chains in the inside of the glob
and the polar side chains outside in the polar
solvent medium. Figure 26.30
58
Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.3 PEPTIDE CHEMISTRY (page 1362)
• 26.3a Nomenclature and Structure

An example
Lactate dehydrogenase Figure 26.31
59
Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.3 PEPTIDE CHEMISTRY (page 1363)
• 26.3a Nomenclature and Structure
• Biological activity of proteins largely
  determined by its tertiary structure (shape).
• Pockets or bays (active sites) allow
  transportation and reactions of selected
  molecules.

A binding site in protein captures (binds) a
small molecule for transport, or reaction with an
appropriately located reactive site. Figure 26.31
60
Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.3 PEPTIDE CHEMISTRY (page 1363)
• 26.3a Nomenclature and Structure

• Biological activity of proteins largely
  determined by its tertiary structure (shape).
• Denaturation (irreversibly disrupting of tertiary
  structure) leads to loss of biological activity.
• Heating (boiling an egg)
• pH change (curdling of milk)
• Denaturation may also be reversible
• treatment with thiols

61
Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.3 PEPTIDE CHEMISTRY (page 1363)
• 26.3a Nomenclature and Structure

One method of denaturing proteins, of destroying
the secondary and tertiary structure, is to break
the disulfide bonds. If air oxidation re-forms
the disulfides, the higher order structures are
regenerated and biological activity is
reestablished. Figure 26.33
62
Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.3 PEPTIDE CHEMISTRY (page 1362)
• 26.3a Nomenclature and Structure

Some proteins do even have a quarternary
structure as the result of combinations of
smaller polyamino acid units. V.d. Waals and
electrostatic forces keep these units together in
a super structure.
Example Hemoglobine
63
Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.3 PEPTIDE CHEMISTRY (page 1363)
• 26.3a Nomenclature and Structure

The quaternary structure of hemoglobin. Figure
26.35
64
Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.3 PEPTIDE CHEMISTRY (page 1363)
• 26.3a Nomenclature and Structure

The unoxidized and oxidized heme structures of
hemoglobin Figure 26.34
65
Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.3 PEPTIDE CHEMISTRY (page 1363)
• 26.3a Nomenclature and Structure

General Problems in Protein Chemistry

• How do we determine the primary structure of an
  unknown protein?
• If protein structure is known, how can we
  synthesize it?

66
Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.3 PEPTIDE CHEMISTRY (page 1364)
• 26.3b Determination of Protein Structure

• X-ray diffraction analysis.
• Cleavage of a protein to the constituent amino
  acids.
• Determination of the actual sequence of the amino
  acids in the protein.

67
Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.3 PEPTIDE CHEMISTRY (page 1364)
• 26.3b Determination of Protein Structure

?
Cleavage of a hexapeptide to its constituent
amino acids. Figure 26.35
68
Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.3 PEPTIDE CHEMISTRY (page 1364)
• 26.3b Determination of Protein Structure

Usually, a first separation is carried out when
the disulfide bonds are broken!
Cleavage of a hexapeptide to its constituent
amino acids. The disulfide bonds are first broken
to produce two fragments, which are hydrolyzed to
break the amide bonds. Figure 26.35
69
Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.3 PEPTIDE CHEMISTRY (page 1364)
• 26.3b Determination of Protein Structure

Separation Techniques
Electrophoresis
Gel-filtration chromatography
Ion-exchange chromatography
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Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.3 PEPTIDE CHEMISTRY (page 1364)
• 26.3b Determination of Protein Structure

A schematic description of chromatographic
separation of polyamino acids. Figure
26.37
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Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)
Qualitative and Quantitative analysis of amino
acids

• 26.3 PEPTIDE CHEMISTRY (page 1364)
• 26.3b Determination of Protein Structure

Polypeptides can be hydrolyzed to constituent
amino acids, which can be separated by
chromatography. Reaction of each amino acid with
ninhydrin gives a purple color that can be
quantitatively analyzed spectroscopically. The
intensity of the purple color is proportional to
amount of amino acid formed. Figure 26.38
72
Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.3 PEPTIDE CHEMISTRY (page 1364)
• 26.3b Determination of Protein Structure

Polypeptides can be hydrolyzed to constituent
amino acids, which can be separated by
chromatography. Reaction of each amino acid with
ninhydrin gives a purple color that can be
quantitatively analyzed spectroscopically. The
intensity of the purple color is proportional to
amount of amino acid formed. Figure 26.38
73
Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.3 PEPTIDE CHEMISTRY (page 1366)
• 26.3b Determination of Protein Structure

Determination of the actual sequence of the amino
acids in the protein
Sanger Degradation
For the amino terminus
74
Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.3 PEPTIDE CHEMISTRY (page 1367)
• 26.3b Determination of Protein Structure

The amino acid at the amino terminus can be
identified by reaction with 2,4-dinitrofluorobenze
ne, followed by hydrolysis. Only the amino acid
at the amino end of the chain will be
labeled. Figure 26.39
75
Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.3 PEPTIDE CHEMISTRY (page 1367)
• 26.3b Determination of Protein Structure

Problem 26.18 What is the mechanism of adduct
formation in Figure 26.39. What is the function
of the nitro groups (Chapter 14, 671)?
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Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.3 PEPTIDE CHEMISTRY (page 1366)
• 26.3b Determination of Protein Structure

Determination of the actual sequence of the amino
acids in the protein
Enzymatic cleavage using
Carboxypeptidase
For the carboxy terminus
77
Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.3 PEPTIDE CHEMISTRY (page 1367)
• 26.3b Determination of Protein Structure

Carboxypeptidase is an enzyme that cleaves only
at the carboxy end of a polypeptide. Figure
26.40
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Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.3 PEPTIDE CHEMISTRY (page 1367)
• 26.3b Determination of Protein Structure
• A more stepwise degradation method step by step
  sequencing

Edman Degradation
79
Isothiocyanates react with amines to give
thioureas. Phenylisothiocyanate can be used to
label the amino terminus of a polypeptide. Figur
e 26.42
80
The Edman procedure for sequencing polyamino
acids uses phenylisothiocyanate. The amino
terminus is identified by the structure of the
phenylthiohydantoin formed. Notice that this
method does not destroy the peptide chain as
does the Sanger procedure. Figure 26.43
81
Problem 26.20 Provide a mechanism for the
formation of the phenylthiohydantion from the
thiazolinone (Fig 26.43)
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Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.3 PEPTIDE CHEMISTRY (page 1370)
• 26.3b Determination of Protein Structure
• A more stepwise degradation method step by step
  sequencing

The structures of polyamino acids can be
determined through repeated applications of the
Edman procedure, which is one method of
sequencing. Figure 26.44
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Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.3 PEPTIDE CHEMISTRY (page 1370)
• 26.3b Determination of Protein Structure
• The use of chemical enzymes cleavage of
  peptide chain at certain amino acids.

Reacts specifically with sulfur containing amino
acids
The structures of polyamino acids can be
determined through repeated applications of the
Edman procedure, which is one method of
sequencing. Figure 26.44
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Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)
Mechanism?
The carboxy end of each methionine is cleaved on
treatment of a polypeptide with cyanogen with
cyanogen bromide (BrCN). Figure 26.45
85
The mechanism of cleavage using BrCN. Figure
26.46
86
The mechanism of cleavage using BrCN. Figure
26.46
87
Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.3 PEPTIDE CHEMISTRY (page 1371)
• 26.3b Determination of Protein Structure
• The use of enzymes cleavage of peptide chain at
  certain amino acids.

Chymotrypsin
Cleaves peptides at amino acid positions
containing aromatic side chains
The structures of polyamino acids can be
determined through repeated applications of the
Edman procedure, which is one method of
sequencing. Figure 26.44
88
Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.3 PEPTIDE CHEMISTRY (page 1371)
• 26.3b Determination of Protein Structure
• The use of enzymes cleavage of peptide chain at
  certain amino acids.

Trypsin
The structures of polyamino acids can be
determined through repeated applications of the
Edman procedure, which is one method of
sequencing. Figure 26.44
89
Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.3 PEPTIDE CHEMISTRY (page 1372)
• 26.3b Determination of Protein Structure
• An example of peptide sequencing

An example of peptide sequencing using Sanger and
Edman procedures as well as enzymatic cleavage
reactions. Figure 26.47
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Introduction to Amino Acids and Polyamino Acids
(Peptides and Proteins)

• 26.3 PEPTIDE CHEMISTRY (page 1372)
• 26.3b Determination of Protein Structure
• An example of peptide sequencing

Problem 26.21 The nonapeptide bradykinin can be
completely hydrolyzed in acid to give three
molecules of Pro, two molecules each of Arg en
Phe, and single molecules of Ser and Gly.
Treatment with chymotrypsin gives the
pentapeptide Arg.Pro.Pro.Gly.Phe, the tripeptide
Ser.Pro.Phe, and Arg. End-group analysis shows
that both the amino and carboxy termini are the
same. Provide the sequence for bradykinin.
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• 26.3 PEPTIDE CHEMISTRY (page 1372)
• 26.3c Synthesis of Peptides

Required High yields High selectivity
An example of peptide sequencing using Sanger and
Edman procedures as well as enzymatic cleavage
reactions. Figure 26.47
92
The possible combinations of two unprotected
amino acids. Figure 26.48
93
Suggest a method to achieve selectivity.
The possible combinations of two unprotected
amino acids. Figure 26.48
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• 26.3 PEPTIDE CHEMISTRY (page 1373)
• 26.3c Synthesis of Peptides
• Activation of one the amino acids.

Some specificity may be obtained by allowing the
acid chloride of one amino acid (activated) to
react with another amino acid. Figure 26.49
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• 26.3 PEPTIDE CHEMISTRY (page 1374)
• 26.3c Synthesis of Peptides
• Activation of one the amino acids.

Here, too, more than one product is
inevitable. Figure 26.50
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• 26.3 PEPTIDE CHEMISTRY (page 1374)
• 26.3c Synthesis of Peptides
• Activation of one carboxy group and block others!

In any successful strategy, we must activate the
carboxy end and block the amino end of one amino
acid while blocking reaction at the carboxy end
of the other amino acid. Figure 26.51
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• 26.3 PEPTIDE CHEMISTRY (page 1375)
• 26.3c Synthesis of Peptides
• Blocking/Deactivation of Amino Groups

In any successful strategy, we must activate the
carboxy end and block the amino end of one amino
acid while blocking reaction at the carboxy end
of the other amino acid. Figure 26.51
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• 26.3 PEPTIDE CHEMISTRY (page 1375)
• 26.3c Synthesis of Peptides
• Deactivation of amino functions

Two protecting, or blocking groups for amine ends
of amino acids. Figure 26.52
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• 26.3 PEPTIDE CHEMISTRY (page 1375)
• 26.3c Synthesis of Peptides
• Deactivation of carboxy functions

How?
A carboxy end can be protected as a simple
ester. Figure 26.53
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• 26.3 PEPTIDE CHEMISTRY (page 1375)
• 26.3c Synthesis of Peptides
• Coupling of both protected amino acids

Very efficient by using
Dicyclohexylcarbodiimide
DCC
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• 26.3 PEPTIDE CHEMISTRY (page 1376)
• 26.3c Synthesis of Peptides
• Coupling of both protected amino acids

Coupling can be achieved using dicyclohexylcarbodi
imide (DCC). Figure 26.54
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Mechanism?
Coupling can be achieved using dicyclohexylcarbodi
imide (DCC). Figure 26.54
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The mechanism of amino acid coupling using
DCC. Figure 26.56
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• 26.3 PEPTIDE CHEMISTRY (page 1376)
• 26.3c Synthesis of Peptides
• Reaction of cumulated polarized double bonds with
  nucleophiles.

The mechanism of amino acid coupling using
DCC. Figure 26.55
105
The mechanism of amino acid coupling using
DCC. Figure 26.56
106
Now deprotection!
The mechanism of amino acid coupling using
DCC. Figure 26.56
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• 26.3 PEPTIDE CHEMISTRY (page 1377)
• 26.3c Synthesis of Peptides
• Reaction of cumulated polarized double bonds with
  nucleophiles.

Methods for removing the protecting groups used
in our scheme. Figure 26.57
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• 26.3 PEPTIDE CHEMISTRY (page 1377)
• 26.3c Synthesis of Peptides
• Reaction of cumulated polarized double bonds with
  nucleophiles.

Methods for removing the protecting groups used
in our scheme. Figure 26.57
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• 26.3 PEPTIDE CHEMISTRY (page 1378)
• 26.3c Synthesis of Peptides
• Peptide synthesis is a repetitive procedure and
  therefore can be automated!

Peptide Synthesis on Polystyrene
Merrifield Procedure
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Polystyrene can be chloromethylated in a
Friedel-Crafts procedure, and the chlorines
replaced through SN2 reaction with the
unprotected carboxy end of an amino acid. This
technique anchors an amino acid to the polymer
chain. Figure 26.58
111
The steps of amino acid synthesis can now be
carried out on this immobilized amino
acid. Figure 26.59
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• 26.3 PEPTIDE CHEMISTRY (page 1378)
• 26.3c Synthesis of Peptides
• Detachment of peptide from polymer

When the synthesis is complete, the polypeptide
can be detached from the polymer backbone by
reaction with HF Figure 26.60
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• 26.3 PEPTIDE CHEMISTRY (page 1379)
• 26.3c Synthesis of Peptides

Peptides are now routinely produced on
commercially available Polypeptide Synthesizers
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• 26.3 SOMETHING MORE NUCLEOSIDES, AND NUCLEIC
  ACIDS (page 1380)

Protein synthesis in vivo directed by nucleic
acids DNA and RNA
DNA deoxyribonucleic acid RNA ribonucleic acid
Nucleotides phosphorylated nucleosides
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• 26.3 SOMETHING MORE NUCLEOSIDES, AND NUCLEIC
  ACIDS (page 1380)

A nucleoside ?-glycoside of a sugar and
heterocyclic molecule (base)
The sugars ribose and dexoxyribose, and the
corresponding nucleosides and nucleotides,
phophorylated nucleosides. Figure 26.61
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• 26.3 SOMETHING MORE NUCLEOSIDES, AND NUCLEIC
  ACIDS (page 1380)

Only five bases are employed by nature!
117
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• 26.3 SOMETHING MORE NUCLEOSIDES, AND NUCLEIC
  ACIDS (page 1382)

Nucleic acids have like proteins high ordered
structures by formation of distinct base paires.
In DNA A always combines with T G always
combines with C
Adenine-thymine and guanine-cytosine form base
pairs through effective hydrogen-bond
formation. Figure 26.61
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• 26.3 SOMETHING MORE NUCLEOSIDES, AND NUCLEIC
  ACIDS (page 1382)

The bases on one strang of DNA determines the
structure of another strang.
The sequence of nucleotides on one polymer
determines the sequence in another through
formation of hydrogen-bonded base pairs, C-G and
A-T. Figure 26.61
120
Watson and Crick DNA is a double-stranded helix!
The famous double helix is held together by
hydrogen bonds between base pairs. Figure
26.66
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• 26.3 SOMETHING MORE NUCLEOSIDES, AND NUCLEIC
  ACIDS (page 1382)

• Two major questions
• Where does the density of information come from
  that controls the synthesis of complex proteins?
• What is the actual mechanism of the information
  transferal?

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Replication of DNA
Figure 26.67
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Protein Synthesis by production of messenger RNA
Synthesis of mRNA. Figure 26.68
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Protein Synthesis by production of messenger RNA
One or more sequences of three bases (codons) in
the mRNA determine the synthesis of the amino
acids to build up the protein. Table 26.2
Synthesis of mRNA. Figure 26.68
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• 26.7 ADDITIONAL PROBLEMS (page 13902)

All problems 26.26-26.42