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Amino acids and peptides
The “Lego” of proteins
Amino Acids
• Same general
structure
• Called alpha amino
acids
• L- isomer is
physiologically active
• Side chain or R group
determines other
properties
• Acid-base properties
O
H3N+
O
R
Amino Acids, General
• pK of carboxyl group around 2.3
– Deprotonated at physiological pH
• R – COO-
• pK of amino group around 9.5
– Protonated at physiological pH
• H3N+-R
• Some R-groups are acidic or basic
Nonpolar amino acids
O
NH3+
C
H2
NH3+
H
C
O
glycine(G)
O
H2C
H
C
H3C
Leucine (L)
O
O
CH3
CH3
Valine (V)
O
H
+
H
N
NH3+
O
H3C
CH3
NH3+
CH3
Alanine (A)
O
NH3+
O
O
C
H CH
2
H3C
Isoleucine (I)
Proline (P)
O
O
Aromatic Amino Acids
O
O
H3N+
H3N+
O
HO
phenylalanine (F)
pKr = 10.07
tyrosine (Y)
O
H3N+
O
O
N
tryptophan (W)
Polar Amino Acids, alcohols
O
H3N+
HO
Serine (S)
O
O
H3N+
H3C
O
OH
Threonine (T)
Polar Amino Acids
(sulfur containing)
O
O
H3N+
O
N3N+
O
HS
S
Cysteine (C)
H3C
Methionine (M)
Polar amino acids (amides)
O
H3N+
O
O
H3N+
O
H2N
O
Asparagine (N)
H2N
O
Glutamine (Q)
Charged Amino Acids (Acidic)
O
H3N+
O
O
H3N+
O
O
O
Aspartate (D)
pKr = 3.86
O
O
Glutamate (E)
pKr = 4.25
Charged Amino Acids (Basic)
O
H3N+
O
O
H3N+
O
H3N+
O
HN
N
HN
NH2+
NH3+
H2N
Arginie (R)
pKr = 12.48
Histidine (H)
pKr = 6.0
Lysine (K)
pKr = 10.53
O
Titration of Amino acids
• Titration of glycine
Titration of Glutamate
O
pK = 9.67 H3N+
O pK = 2.19
O
O
Glutamate (E)
pKr = 4.25
Purification of amino acids
• Chromatography
– Various types
– Ion exchange
• Uses net charge or can change with pH
– Separate K, D and A
– HPLC
Electrophoresis
• Using electricity to move particles through
a gelatinous matrix
• Isoelectric point
• IEF
Peptides
• Peptide bond is amide linkage between amino acids
• No free rotation about C-N bond due to partial double
bond character of bond
– resonance
peptide bond
H3N+
O
O
N
H
R1
-
O
O
H3N+
R2
O
+
O
N
R1
R2
Tetrapeptide
• Note planes of peptide bonds
Peptides
• Peptides are vectorial
– Have N and C termini
• Sequences read H3N+---COOP-I-G
O
H2N+
O
N
H
O
N
H
O
Draw a tetrapeptide of L-A-R-D
at physiological pH
• Answer
Biologically Interesting Peptides
• Aspartame
– L-aspartyl-Lphenylalanine methyl ester
O
H3N+
O
O
N
H
O
O
CH3
Other small interesting peptides
• Enkephalins
Y-G-G-F-L
Y-G-G-F-M
• Oxytocin
C-Y-I-Q-N-C-P-L-G-NH2
• Has C—C disulfide
• Vasopressin
C-Y-F-Q-N-C-P-R-G-NH2
• Also disulfide
Chemical Synthesis of Peptides
• Why?
• Done solid phase
– Problem with in solution
• Hard to make pure desired sequence
– Purify by filtration
• Side chains blocked
• Made backwards ( C---N)
Scheme for peptide synthesis
Tetrapeptide answer
A
L
O
H3N+
O
N
H
D
R
O
N
H
O
N
H
O
O
NH
H2N+
• Back
NH2
O
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