Download Amino Acids

Amino Acids
amine
H2N
O
C
OH
C H
carboxylic acid
H
R
R varies with amino acid
R = H glycine
Nonpolar R-groups
glycine -H
alanine -CH3
valine
-CH-CH3
CH3
CO2H
H2N C H
R
proline
 COOH
N
H
2o amine
leucine -CH2-CH-CH3
CH2
CH3
phenylalanine
isoleucine -CH-CH2-CH3
CH3
methionine -CH2-CH2-S-CH3
Polar R-groups
serine -CH2-OH
threonine -CH-CH3
OH
tyrosine
CH2
asparagine -CH2-C-NH2
O
glutamine -CH2-CH2-C-NH2
O
OH
cysteine -CH2-SH
tryptophan
CH2
NH
Acidic R-groups
glutamic acid -CH -CH -C O
2
2
OH
O
aspartic acid -CH2-C
OH
Basic R-groups
lysine -CH2-CH2-CH2-CH2-NH2
=
arginine -CH2-CH2-CH2-NH-C-NH2
NH
histadine
CH2
H
N
N
Amino acids
O
C
HH32NN+
glycine non-chiral
O
OH
C H
H
R
all other -amino acids in proteins
at neutral pH (pH = 7.0) zwitterion
very high b.p. (> 200oC)
very soluble in water
L-enantiomers
acid-base chemistry
O
O
C
H3N+
OH
C H
R
C
H32N+
C
R
OH
O
H
O
C
H2N
OC H
R
low pH
neutral pH
high pH
amine and c.a. amine protonated amine and c.a.
c.a. deprotonated deprotonated
protonated
negative charge
positive charge no net charge
isoelectric point pH = pHI
amino acids
diprotic acids 2 pKa
Titration of an amino acid
alanine R = CH3
O
C
pKa2 = 9.69 H3N+
Ka1 = [H+][A-]
[HA]
OH
C H
CH
R 3
0.1 M
4.57 x 10-3 = x2
0.1 - x
X = 2.14
x
10-2
pKa1 = 2.34
+]
[H
=
Ka1 = 10-2.34 = 4.57 x 10-3
[H+] [A-] [HA]
initial 0
change +x
equil. +x
0
+x
+x
pH = 1.87
0.1
-x
0.1-x
+1
O
net charge
C
OH
H3N C H
+
9.0
8.0
pH
CH3
7.0
6.0
5.0
4.0
3.0
2.0
1.0
O
C
-
O
+
H3N C H
×
CH3
0
equivalents of OH-
O
net charge
+1
+1/2
9.0
8.0
pH
OH
0.05 M
H3N C H
+
CH3
O
7.0
6.0
5.0
4.0
3.0
2.0
1.0
C
C
pKa1 = 2.34
O+
H3N C H
×
0
×
1/2
equivalents of OH-
0.05 M
0.05 M
pH = pKa + log [A-]
[HA]
0.05 M
pH = pKa = 2.34
CH3
net charge
+1
pH
9.0
8.0
7.0
6.0
5.0
4.0
3.0
2.0
1.0
+1/2
0
at equivalence point:
pKa2 = 9.69 O pKa1 = 2.34
C
-
O
+
H3N C H
×
CH3
isoelectric point
×
0
×
1/2
1
equivalents of OH-
pH = pKa1 + pKa2
2
pH = (2.34 + 9.69)/2
pH = pHI = 6.02
net charge
+1
+1/2
0
O
-1
C
OH3N+ C H
CH3
7.0
6.0
5.0
4.0
3.0
2.0
1.0
-1/2
×
9.0
8.0
pH
at 2nd half-way point:
×
pKa2 = 9.69
O
C
×
0
OH2N C H
×
CH3
1/2
1
3/2
equivalents of OH-
pH = pKa2 = 9.69
resonance structure
amides
O
O
C
C
N
N
dipeptide
H
H2N C C
O
OH
H
H2N C C
CH3
H
alanine
glycine
H
O
OH
H2N C C
CH3
O
H
N C C
H H
Ala-Gly
+H2O
O
OH
Proteins
“backbone”
_
_
_
_
_
_
H R
H R
H R
_
H N1-C1-C1-N2-C2-C2-N3-C3-C3- OH
O
O
O
peptide bonds
C-terminal
N-terminal
residue
residue
=
=
=
biological activity = structure
4 levels
protein structure
Primary structure = order of the amino acids
Secondary structure
hydrogen bonding backbone groups
=
=
=
H-bond donors
_
_
_
_
_
_
H R
H R
H R
_
H N1-C1-C1-N2-C2-C2-N3-C3-C3- OH
O
O
O
H-bond acceptors
Two main secondary structures:
-helix
-sheet
Alpha helix
Every C=O bonded to N-H 4 residues away
forms a helix
core is backbone
R-groups outside
3.6 amino acids per turn
H
proline
=
C
=
C
O
O
N
no H-bonding
breaks helix
Beta sheet
Every C=O bonded to N-H far apart in 1o structure
on different chains
peptide chains extended
side-by-side
maximal H-bonding for anti-parallel chains
small R-groups above and below the sheet
if not -helix or -sheet
random coil
glutamic acid R = - CH2CH2COOH
O
C
H3N+
OH
C H
pKa1 = 3.20 (-COOH)
O
CH
CH2C
pK
=
4.25
(R-COOH)
R
2
a2
pKa3 = 9.67
OH
(-NH3)
It will take ___
3 equivalents to titrate glutamic acid
1st group
2nd group
3rd group
+1
0
-2
-1
12
C
O
OH
H3N+ C H
10
×
8
pH
×
pHI = 3.7
4
×
×
×
2
1
2
equivalents OH-
CH2CH2C
O
OH
pKa1 = 3.20
pKa2 = 4.25
pKa3 = 9.67
3.2 + 4.25 = 3.7
2
4.25 + 9.67 = 7.0
2
3