Chapter Outline
Amino Acids
Amino acid classes
Bioactive AA
Modified AA
Peptides
Proteins
Protein structure
Fibrous proteins
Globular proteins
Stereoisomers
Titration of AA
AA reactions
5P1-1
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
5P1-2
Definition, cont.
If the R group is not H, the AA can
exist in two enantiomeric forms
(nonsuperimposable mirror image)
forms.)
O
C
+
H3 N
a carbon
C
R1
O
O
H
H
Mirror plane
O
C
C
+
NH3
R1
5P1-3
Amino Acids
General form: 1. an amino
acid (AA); 2. two AA linked to
form the peptide bond.
O
C
+
H3N
L-form
C
R1
HO H HO
+
H3N C C N C C O
R1
R1
H
O
PEPTIDE BOND
5P1-4
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
5P1-5
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
5P1-6
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
5P1-7
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
5P1-8
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
C
O
NH2
glutamine, Gln
tyrosine, Tyr
OH
5P1-9
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
5P1-10
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.
5P1-11
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.
5P1-12
Titration of Alanine
B=C
pK2=9.73
10
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
2
5P1-13
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.
5P1-14
Isoelectric point-2
In general the pI
is the average
of the two
pKa’s
bracketing the
isoelectric
structure.
Eg.: glutamic
acid, pI = 3.2
pK3=9.9
pK2=4.3
pK1=2.2
5P1-15
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
H O
H O
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
5P1-16
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
C
H
H
+
a
a
C N
C N
Ca
Ca
- O
O
5P1-17
Peptides-3
The peptide bond
angles force specific
conformations of
proteins and, on
extended chains,
successive R groups
are on opposite
sides.
5P1-18
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
5P1-19
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.
5P1-20
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
5P1-21
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
|
8
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.
5P1-22