Amino Acids
and Proteins
• Proteins are composed of amino acids.
• There are 20 amino acids commonly
found in proteins. All have:
H
NH2
Cα COOH
R
Amino acids at neutral pH are dipolar ions
(zwitterions) because their α-carboxyl and
α-amino groups are ionized.
H
+
NH3
C
R
COO
Titration curve for Glycine:
pK22
8
pH
NH
3+ =
NH3+
NH2
NH
6
pK11
4
COOH=
COO-
2
0. 5 [NaOH]
pK22
8
pH
6
4
2
NH
NH3+
pK11
COOH
Isoelectric
point (no net
charge)
0. 5 [NaOH]
pKa Values of the Amino Acids
You should know these numbers and know
what they mean!
• Alpha carboxyl group - pKa = 2
• Alpha amino group - pKa = 9
• These numbers are approximate, but
entirely suitable for our purposes.
Aliphatic Non-Polar Amino Acids
COO-
-
COO
H N
C
H CH2
H2C
CH2
+
2
Proline (Pro, P)
COOH3+N - C - H
CH3
Alanine (Ala, A)
COO
COO-
H N- C - H
H3+N - C - H
-
+
3
H3+N - C - H
CH
CH3 CH3
Valine (Val, V)
COOH3+N - C - H
CH2
CH2
H - C - CH3
CH
CH3 CH3
CH2
S
CH3
CH3
Leucine (Leu, L)
Isoleucine (Ile, I)
CH2
Methionine (Met, M)
Aromatic Non-Polar Amino Acids
COO-
COO-
H3+N - C - H
H3+N - C - H
CH2
CH2
C
CH
Phenylalanine (Phe, F)
N
H
Tryptophan (Trp, W)
Polar Uncharged Amino Acids
COO-
COO-
COO-
H3+N - C - H
H3+N - C - H
H3+N - C - H
H
CH2OH
Glycine (Gly, G)
-
COO
+
3
H N- C - H
CH2
Serine (Ser, S)
pKa=13
COOH3+N - C - H
CH2
OH
Tyrosine (Tyr, Y)
pKa=10.1
SH
Cysteine (Cys, C)
pKa=8.3
CHOH
CH3
Threonine (Thr, T)
pKa=13
Polar Uncharged Amino Acids
-
COO
COO-
H N- C - H
H3+N - C - H
+
3
O
CH2
CH2
C
CH2
C
NH2
Asparagine (Asn, N)
O
NH2
Glutamine (Gln, Q)
Acidic Amino Acids
COO-
COO-
H3+N - C - H
H3+N - C - H
O
CH2
CH2
C
CH2
O-
Aspartate (Asp, D)
C
O
O-
Glutamate (Glu, E)
pKa=3.9
pKa=4.3
Basic Amino Acids
COO-
COO-
COO-
H3+N - C - H
H3+N - C - H
H3+N - C - H
CH2
CH2
CH2
CH2
NH3+
CH2
CH2
CH2
NH
C
H2+N
NH2
Lysine (Lys, K)
Arginine (Arg, R)
pKa=10.5
pKa=12.5
CH2
HC=
HC C
N
NH
C
H
Histidine (His, H)
pKa=6.0
Serine and Threonine can be PHOSPHORYLATED:
COO-
ATP
ADP, Pi
H3+N - C - H
H3+N - C - H
CH2OPO32-
CH2OH
phosphoserine
serine
COOH3+N - C - H
COO-
ATP
ADP, Pi
COOH3+N - C -
H
CHOH
CHOPO32-
CH3
CH3
threonine
phosphothreonine
Disulfide Bond:Two cysteine
COOH3+N - C - H
CH2
S
S
CH2
H3+N - C - H
COO-
Cystine
residues condense. Disulfide
bonds may occur between
cyteine residues within the
same protein (intrachain) or
between two cysteine residues
occuring in different proteins
(interchain). Disulfide
formation is a major factor in
the determination of protein
structure.
Permanent waving is the result
of the reduction of disulfides in
the α-keratin protein (that hair is
made of) and spontaneous
re-oxidation of those disulfide
bonds in air.
Uncommon Amino Acids
•
•
•
•
Hydroxylysine, hydroxyproline - collagen
Carboxyglutamate - blood-clotting proteins
Pyroglutamate - bacteriorhodopsin
Phosphorylated amino acids - signaling
device
Titration of Glutamic Acid
Titration of Lysine
A Sample Calculation
What is the pH of a glutamic acid solution if
the alpha carboxyl is 1/4 dissociated?
• pH = 2 + log10 [1]
¯¯¯¯¯¯¯
[3]
• pH = 2 + (-0.477)
• pH = 1.523
Another Sample Calculation
What is the pH of a lysine solution if the side
chain amino group is 3/4 dissociated?
• pH = 10.5 + log10 [3]
¯¯
¯¯¯¯¯
[1]
• pH = 10.5 + (0.477)
• pH = 10.977 = 11.0
Reactions of Amino Acids
• Carboxyl groups form amides & esters
• Amino groups form Schiff bases and
amides
• Side chains show unique reactivities
– Cys residues can form disulfides and can be
easily alkylated
– Few reactions are specific to a single kind of
side chain
Stereochemistry of Amino Acids
• All but glycine are chiral
• L-amino acids predominate in nature
• D,L-nomenclature is based on D- and Lglyceraldehyde
• R,S-nomenclature system is superior,
since amino acids like isoleucine and
threonine (with two chiral centers) can be
named unambiguously
Spectroscopic Properties
• All amino acids absorb in infrared region
• Only Phe, Tyr, and Trp absorb UV
• Absorbance at 280 nm is a good
diagnostic device for amino acids
• NMR spectra are characteristic of each
residue in a protein, and high resolution
NMR measurements can be used to
elucidate three-dimensional structures of
proteins
Separation of Amino Acids
• Mikhail Tswett, a Russian botanist, first
separated colorful plant pigments by
‘chromatography’
• Many chromatographic methods exist for
separation of amino acid mixtures
– Ion exchange chromatography
– High-performance liquid chromatography