Download Amino Acids and Peptides

Amino Acids,
1
Chapter Outline

Amino Acids
– Amino acid classes (G1)
– Stereoisomers (G2)
– Bioactive AA
– Titration of AA (G3)
– Modified AA
– AA reactions
Peptides
 Proteins

– Protein structure
– Fibrous proteins
– Globular proteins
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5.1 Amino Acid: Definition
An alpha amino acid is a carboxylic acid with an
amino group on the carbon alpha to the
carboxylic acid .
 The alpha carbon also has an R group side chain
except for glycine which has two Hs.

O
Generic amino
acid at physiological
pH: zwitterion form
C
O
+
H3N C H
R
aC
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Definition, cont.
 If
the R group is not H, the AA can
exist in two enantiomeric forms
(nonsuperimposable mirror image)
forms.)
O
O
O
O
C
C
+
H3N
a carbon
C
R1
H
H
Mirror plane
C
+
NH3
R1
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Amino Acids
General
form:
1. an amino acid (AA);
2. two AA linked to form the
peptide bond.
O
C
+
H3N
C
L-form R1
HO H HO
+
H3N C C N C C O
R1
R1
H
O
PEPTIDE BOND
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Amino Acids-2
 Only
the L form of amino acids is
commonly found in proteins.
 Depending on the nature of the R
group, AA are classified into four
groups.
nonpolar
polar
acidic
basic
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AA with nonpolar side chains-1
H3N
+
COO
C
H
CH3
alanine, Ala
H3N
+
H3N
+
COO
C
CH2
phenylalanine, Phe
COO
C
H
CH2
CH
CH3 CH3
leucine,Leu
H
H3N
+
COO
C
H
CH3 CH
CH2
CH3
isoleucine, Ile
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AA with nonpolar side chains-2
H 3N
+
COO
C H
CH
CH3 CH3
valine, Val
COO
H 2N
+
CH2
C H
CH2
CH2
proline, Pro
H 3N
+
COO
C
H
CH2CH2S CH3
methionine, Met
COO
H 3N
+
C H
CH2
C
CH
N
H
tryptophan, Trp
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AA with nonpolar side chains-2
Contain hydrocarbon R groups.
 Hydrocarbons side chain can be aromatic
or aliphatic.
 Interact poorly with water.
 Also refer as hydrophobic amino acids.

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AA with polar side chains-1
H3N
+
COO
C
H
H
Glycine, Gly
H3N
+
H3N
+
COO
C
CH2 OH
Serine, Ser
COO
C
H
CH2 SH
cysteine, Cys
H
H3N
+
COO
C H
CH OH
CH3
threonine, Thr
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AA with polar side chains-2
H3N
+
COO
C H
CH2
O C NH2
asparagine, Asn
H3N
+
COO
C
H
CH2
H3N
+
COO
C H
CH2
CH2
O C NH2
glutamine, Gln
tyrosine, Tyr
OH
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AA with polar side chains-2
Have functional groups that easily interact
with water.
 Functional groups also capable in forming
hydrogen bonding.

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AA: acidic and basic
H3N
+
COO
H3N
C H
CH2
O C O
aspartic acid, Asp
H3N
+
CH2
CH2
NH
+
H2N C NH2
arginine, Arg
C H
CH2 glutamic acid,
CH2 Glu
O C O
COO
C H
CH2
+
COO
H3N
+
COO
C H
CH2
CH2
CH2
CH2
+
NH3
lysine, Lys
H3N
+
H
C
+
HN
COO
C H
CH2
C
NH
C
H
histidine, His
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Acidic AA attached to carboxylate groups
that is negatively charged at
physiologically pH.
 Basic AA bear a positive charge at
physiological pH.
 Basic AA can form ionic bonds with asidic
AA.

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Amino Acid Titration
 At
physiological pH, the carboxyl
group of the AA is negatively charged
and the amino group is positively
charged.
 Amino acids without charged side
chains are zwitterions and have no
net charge. H3+N-CHR-COO-.
 A titration curve shows how the
amine and carboxyl groups react with
hydrogen ion.
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Amino Acid Titration-2
 At
low pH a nonacidic/nonbasic
amino acid is protonated and has
the structure below.
 H3N+CHRCOOH
 The charge behavior of acidic and
basic AAs is more complex.
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Titration of Alanine
B=C
pK2=9.73
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C
O
H3N CHC OH
R1 A
O
+
H3N CH C O
R1 B
O
+
H3N CH1C O
R1 C
+
pH
5
1
B, pI=pH=6.0
A
A=B
pK1=2.3
1
mole base added
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2
Isoelectric point
The isoelectric point (pI) for an AA occurs
when there is no net charge.
 For a neutral AA, the pI is calculated using
the equation pK1 + pK2/2
 Eg.: alanine: 2.34 + 9.7 / 2 = 6.0
 For acidic or basic AAs, the pI is the
average of the two pKa values bracketing
the isoelectric structure.

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Isoelectric point-2
pK3=9.9

In general the pI
is the average of
the two pKa’s
bracketing the
isoelectric
structure. Eg.:
glutamic acid, pI
= 3.2
pK2=4.3
pK1=2.2
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5.2 Peptides

Peptide: a polymer of about 2-100 AAs linked by the
peptide(amide) bond. As the amino group and the
carboxyl group link, water is lost.
H O
H O
H O
+
+
+
H3N C C O H3N C C O H3N C C O
R1
-H2O
R1
-H2O
R1
H O
H O
H O
+
H3N C C N C C N C C O
H
H
R1
R1
R1
Peptide bonds
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Peptides-2
A peptide is written with the N-terminal
end to the left and the C-terminal end to
the right.
 H2N-Tyr-Ala-Cys-Gly-COOH

Name = Tyrosylalanylcysteinylglycine
 The peptide bond is rigid and planar due
to the resonance contribution shown right.

C
a
O
H
C N
Ca
C
a
+ H
C N
Ca
- O
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Peptides-3

The peptide bond
angles force specific
conformations of
proteins and, on
extended chains,
successive R groups
are on opposite
sides.
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Physiologically Interesting Peptides
 carbon
O
+
H3N CH2CH2C NH CH COO
-
-alanyl-L-histidine CH2
C
HC
NH
N C
Common name: carnosine
found in muscle tissue
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Physiologically Interesting Peptides
-
COO
+
O
O
-
H3N CH CH2 CH2 C NH CH C NH CH2COO
CH2
SH
-glutamyl-L-cysteineylglycine
Glutathione: the reduced form
reduces oxidizing agents by dimerizing to
form the disulfide bond with release of 2 H.
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Physiologically Interesting Peptides
Tyr-Gly-Gly-Phe-Leu
N-terminal AA
C-terminal AA
Short form description for a peptide.
Leucine enkephalin: a natural
analgesic found in the brain
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Physiologically Interesting Peptides
H3
3
+
N -Cys-Tyr-Ile
Oxytocin
Induces labor and
aids in forcing milk
from the mammary
glands.
|
|
S
Gln
|
|
S -Cys-Asn
|
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Pro-Leu-Gly-NH2
Vassopressin has a Phe at position 3
instead of Ile and an Arg at position 8
instead of a Leu. Its role is in regulating
blood pressure.
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THE END
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