Lecture 3: Amino Acids
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–
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Bonus seminar today at 3PM 148 Baker (bonus point
assignment due on Wed. in class or electronically by
email)
Quiz next Wed. (9/7)
Introduction to amino acid structure
Amino acid chemistry
Uncharged polar side chains
+
H3N
+
H3N
COOC
H
COOC
CH2
OH
COO-
+
H H3N
C
H
H
C
OH
+
H3N
COO-
C
H
CH2
CH3
Serine
Threonine
H
Ser
Thr
Glycine
S
T
OH
Tyrosine
Gly
Tyr
G
Y
Uncharged polar side chains
+
H3N
COOC
H
R-SH
R-S- + H+
R-OH
R-O- + H+
CH2
SH
Cysteine
Cys
C
Formation of cystine
Uncharged polar side chains
+
H3N
COOC
+
H3N
H
Asparagine
Asn
N
H
CH2
C
NH2
C
CH2
CH2
O
COO-
C
O
NH2
Glutamine
Gln
Q
Amino acids
•
Polar, uncharged amino acids
–
–
–
–
Contain R-groups that can form hydrogen bonds with water
Includes amino acids with alcohols in R-groups (Ser, Thr, Tyr)
Amide groups: Asn and Gln
Usually more soluble in water
• Exception is Tyr (most insoluble at 0.453 g/L at 25 C)
– Sulfhydryl group: Cys
• Cys can form a disulfide bond (2 cysteines can make one cystine)
Charged polar (acidic) side chains
+
H3N
COOC
H
+
H3N
O
Aspartic acid
D
H
CH2
C
Asp
C
CH2
CH2
O
COO-
C
O
O
Glutamic acid
Glu
E
Amino acids
• Acidic amino acids
– Amino acids in which R-group contains a carboxyl
group
– Asp and Glu
– Have a net negative charge at pH 7 (negatively
charged pH > 3)
– Negative charges play important roles
• Metal-binding sites
• Carboxyl groups may act as nucleophiles in
enzymatic interactions
• Electrostatic bonding interactions
Charged polar (basic) side chains
+
H3N
COOC
H
+
H3 N
COOC
H
CH2
CH2
CH2
CH2
CH2
CH2
Lysine
CH2
NH
C
NH2+ NH2
Lys
Arginine
K
Arg
NH3+
R
COO-
+
H3N
C
H
CH2
C
HC
H+N
NH
CH
Histidine
His
H
Amino acids
• Basic amino acids
– Amino acids in which R-group have net positive charges at pH 7
– His, Lys, and Arg
– Lys and Arg are fully protonated at pH 7
• Participate in electrostatic interactions
– His has a side chain pKa of 6.0 and is only 10% protonated at
pH 7
– Because His has a pKa near neutral, it plays important roles as a
proton donor or acceptor in many enzymes.
– His containing peptides are important biological buffers
Nonstandard amino acids
• 20 common amino acids programmed by genetic code
• Nature often needs more variation
• Nonstandard amino acids play a variety of roles: structural,
antibiotics, signals, hormones, neurotransmitters, intermediates in
metabolic cycles, etc.
• Nonstandard amino acids are usually the result of modification of a
standard amino acid after a polypeptide has been synthesized.
• If you see the structure, could you tell where these nonstandard
amino acids were derived from?
Nonstandard amino acids
Nonstandard amino acids
Peptide bonds
•
Proteins are sometimes called polypeptides since they contain many peptide bonds
R1 O
+
H3N
C
OH
C
+
H
H
R2 O
N
C
O-
H
H
+
H3N
C
R1 O
R2 O
C
N
C
H
H
H
C
C
O-
+ H 2O
Structural character of amide groups
•
•
•
Understanding the chemical character of the amide is important since the peptide bond is an
amide bond.
These characteristics are true for the amide containing amino acids as well (Asn, Gln)
Amides will not ionize:
O
R
C
O
NH2
R
C
NH2
Acid-base properties of amino acids
The dissociation of first proton
from the -carboxyl group is
Gly+ + H2O
K1=
Gly0 + H3O+
[Gly0][H3O+]
The dissociation of the second
proton from the -amino group
Gly0 + H2O
K2=
[Gly+]
Gly- + H3O+
[Gly-][H3O+]
[Gly0]
The pKa’s of these two groups are far enough apart that they can
be approximated by Henderson-Hasselbalch
pH = pK1 + log
[Gly0]
[Gly+]
pH = pK2 + log
[Gly-]
[Gly0]
Titration curve of glycine
+
H3N
COO-
C
H
H
Neutral
form
Titration of Gly
COOH
+
H3N
C
H
H
pK1
+
H3N
C
H
Gly+
pH 2.3
COO-
COO-
Gly0
H2N
H
pK2
pH 9.6
C
H
H
Gly-
From the pK values we can calculate the pI (isoelectric point) where
the amino acid is neutral.
pI ≈ average of (pK below neutral+ pK above neutral)
So, for Gly,
pI = (pK1 + pK2)/2
= (2.3 + 9.6)/2 ≈ 6
General rules for amino acid ionization
• Alpha carboxylic acids ionize at acidic pH and have pKs less
than 6; So in titrating a fully protonated amino acid, alpha
carboxylic acids lose the proton first.
• Alpha amino groups ionize at basic pH and have pKs greater
than 8; So after acids lose their protons, amino groups lose their
proton.
• Most of the 20 amino acids are similar to Gly in their ionization
properties because their side chains do not ionize at biological
pHs.
• However, there are 5 exceptions worth noting (the amino acids
with polar charged side chains)
• Glu, Asp, Lys, Arg, His
• Each has 3 ionizible groups and thus, 3 pKs.
Charged polar (acidic) side chains
COOH 2.1
9.5
+
H3N
C
H
COOH 2.0
9.8
+
H3N
C
H
CH2
CH2
CH2
C
O
C
O
OH 4.1
OH 3.9
Aspartic acid
Glutamic acid
Asp
Glu
D
E
How to calculate the pI of a compound
with more than 2 pKs
• Find the amino acid form with no net charge (total charge = 0).
• Take the pK of the amino acid form going towards +1 form as
the lower pK.
• Next find the amino acid form going towards the -1 form.
• Finally, average these two pKs to get the pI.
Titration curve of aspartic acid
The neutral form of Asp is close to pH 2.8
Take the pKs for +1 and -1 from this point and average to get
approximate pI,
pI = (pK3 + pK1)/2 = (2.0 + 3.9)/2 = 2.95
9.2
Charged polar (basic) side chains
COOH 1.8
COOH 2.2
+
H3N
C
H
CH2
CH2
+
H3 N
9.0
CH2
CH2
NH3+
Lysine
Lys
K
C
10.8
H
CH2
CH2
1.8
COOH
9.3 +
C
H3N
H
CH2
CH2
6.0 HC C
NH
NH
H+N
C
CH
+
NH2
NH2
Arginine
12.5
Arg
R
Histidine
His
H
Titration curve of arginine
The neutral form of Asp is close to pH 10.8
Take the pKs for +1 and -1 from this point and average to get
approximate pI,
pI = (pK2 + pK3)/2 = (9.0 + 13.0)/2 = 11.0
Acid-base properties of amino acids
Amino acid
-COOH pKa
-NH3+ pKa
R-group pKa
Gly
2.3
9.6
-
Ala
2.4
9.7
-
Val
2.3
9.6
-
Leu
2.4
9.6
-
Iso
2.4
9.7
-
Met
2.4
9.2
-
Pro
2.1
10.6
-
Phe
1.8
9.1
-
Trp
2.4
9.4
-
Ser
2.2
9.2
13
Thr
2.6
10.4
13
Tyr
2.2
9.1
10.1
Cys
1.7
10.8
8.3
Asn
2.0
8.8
-
Gln
2.2
9.1
-
Asp
2.1
9.8
3.9
Glu
2.2
9.7
4.3
Lys
2.2
9.0
10.5
Arg
2.2
9.0
12.5
His
2.4
9.2
6.0
More rules for amino acid ionization
•
Carboxylic acid groups near an amino group in a molecule have a more
acidic pK than isolated carboxylic groups.
•
Amino groups near a carboxylic acid group also have a more acidic pK
than isolated amines.
•
Aromatic amines like His have a pK about pH 6.
•
When titrating an amino acid that is fully protonated (ie starting at pH =
1), the alpha carboxylic acids lose their proton first (all free amino acids
have this group), then side chain carboxylic acids, then aromatic amine
side chains (His), then alpha amino groups, then side chain amino
groups.
•
These rules apply to small peptides too.
Amino acids are optically active
•
•
•
•
All amino acids are optically active (exception Gly).
Optically active molecules have asymmetry; not superimposable (mirror
images)
Central atoms are chiral centers or asymmetric centers.
Enantiomers -molecules that are nonsuperimposable mirror images
Asymmetry
• Molecules are classified as Dextrorotatory (right handed), D or
Levrotatory (left handed) L depending on whether they rotate the
plane of plane-polarized light clockwise or counterclockwise
determined by a polarimeter
Asymmetry
• Fischer projections are a shorthand way to write molecules with
chiral centers
Asymmetry
• For -amino acids the arrangement of the amino, carboxyl, R,
and H groups about the C atom is related to glyceraldehyde
Asymmetry
• All -amino acids from proteins have the L-stereochemical
configuration
Diastereomers
• Stereoisomers or optical isomers are molecules with different
configurations about at least one of their chiral centers but are
otherwise identical
• Since each asymmetric center in a chiral molecule can have two
possible configurations, a molecule with n chiral centers has 2n
different possible stereoisomers and 2n-1 enantiomeric pairs
• Ex. Threonine and Isoleucine both have two chiral centers, and thus
4 possible stereoisomers.
Diastereomers
*
*
Diastereomers
• Special case: 2 asymmetric centers are chemically identical (2
asymmetric centers are mirror images of one another)
• A molecule that is superimposable on its mirror image is
optically inactive (meso form)
Cahn-Ingold-Prelog or (RS) System
• The 4 groups surrounding a chiral center a ranked as follows:
Atoms of higher atomic number bonded to a chiral center are
ranked above those of lower atomic number.
• Priorities of some common functional groups SH > OH > NH2 >
COOH > CHO > CH2OH > C6H5 > CH3 > 2H > 1H
• Prioritized groups are assigned letters W, X, Y, Z, so that W > X
>Y>Z
• Z group has the lowest priority (usually H) and is used to
establish the chiral center.
• If the order of the groups W X Y is clockwise, as viewed
from the direction of Z, the configuration is (R from the latin
rectus, right)
• If the order of the groups W X Y is counterclockwise, as
viewed from the direction of Z, the configuration is (S from the
latin sinister, left)
Cahn-Ingold-Prelog or (RS) System
Cahn-Ingold-Prelog or (RS) System
Cahn-Ingold-Prelog or (RS) System
Prochiral centers have distinguishable
substituents
• Prochiral molecules can be converted from an achiral to chrial
molecule by a single substitution
• Molecules can be assigned a right side and left side for two
chemically identical substituents.
• True for tetrahedral centered molecules
• Example is ethanol
Prochiral centers
Planar objects can also be prochiral
• Stereospecific additions in enzymatic reactions
• If a trigonal carbon is facing the viewer so that the substituents
decrease in a clockwise manner it is the re face
• If a trigonal carbon is facing the viewer so that the substituents
decrease in a counterclockwise manner it is the si face
• Acetaldehyde example
Nomenclature
• Glx can be Glu or Gln
• Asx can be Asp or Asn
• Polypeptide chains are always described from the N-terminus to
the C-terminus
Nomenclature
• Nonhydrogen atoms of the amino acid side chain are named in
sequence with the Greek alphabet