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Amino Acids
Amino Acid Structure
• Basic Structure:– (α) Carbon– Carboxylic Acid Group– Amino Group– R-group Side Chain
• Determines properties of Amino Acid
R |
H2N — C —COOH |
H
R Group Classification:- Non-polar, Polar, Aromatic,
Acidic, and Basic
Non-Polar; Hydrophobic
• Glycine (G)• Alanine (A)• Proline (P)• Valine (V)• Leucine (L)• Isoleucine (I)• Methionine (M)
Polar; Hydrophilic
• Serine (S)• Threonine (T)• Cysteine (C)• Asparagine (N)• Glutamine (Q)
Aromatic
• Phenylalanine (F)– Hydrophobic
• Tyrosine (Y)– Hydrophilic
• Tryptophan (W)– Hydrophobic
Charged R-Groups
• Acidic (positively-charged)– Aspartate (D)– Glutamate (E)
• Basic (negatively charged)– Lysine (K)– Arginine (R) - strongly– Histidine (H) - weakly
7
The Peptide Bond
Amide bond formed by the –COOH of an amino acid and the –NH2 of the next amino acid
O CH3
+ | | + |NH3–CH2–COH + H3N–CH–COO–
O CH3 + | | |
NH3–CH2–C – N–CH–COO–
| peptide bond H
8
Peptides
• Amino acids linked by amide (peptide) bonds
Gly Lys Phe Arg Ser
H2N- -COOH
end Peptide bonds end
Glycyllysylphenylalanylarginylserine
Isoelectric Point• Each amino acid has an isoelectric point, (pI) numerically equal to the pH
at which the zwitterion concentration is at a maximum.• The amino acid has no NET charge at its pI; it has one positive and one
negative charge.• At a pH less than the value of the isoelectric point, the amino acid is
protonated and has a POSITIVE charge; at a pH greater than the pI the amino acid is deprotonated and has a NEGATIVE charge.
Cation Neutral Anion
(zwitterion form)
C
H3N H
R
O OC
H3N H
R
O OHC
H2N H
R
O O
H OH
@ pH = pI@ pH < pI @ pH > pI
Prentice Hall c2002 Chapter 3 10
Fig 3.6 Titration curve for alanine
• Titration curves are used to determine pKa values
• pK1 = 2.4
• pK2 = 9.9
• pIAla = isoelectric point
Prentice Hall c2002 Chapter 3 11
Fig 3.7 Ionization of Histidine
(a) Titration curve of histidine
pK1 = 1.8pK2 = 6.0pK3 = 9.3
Derivatization with Ninhydrin
H3N C CO
H O
R(any)
O
O
OH
OH2 +
O
ON
O
O
Ninhydrin (2 mol) reacts with one mol of ANY amino acid to givethe SAME blue colored product. This reaction is performed post-column, after Ion Exchange Chromatography separation of a mixture of amino acids. The area of each peak in the chromatogram is proportional to the relative molar amount of the amino acid of that retention time.
Disulfide bonding in peptidesC C
OH
CH2
H
NN C C
H O
CH3 CH2CH2SCH3
H O
CCN
H
C C
OH
H
N
H
C C
OH
CH(CH3)2
N
HH
N
CH3
H O
CC
SH
H
CC
O H
CH2OH
H
N CC
HO
CH3
CC
O H
H
N
H
CC
O H
CH(CH3)2
N
H H
N
CH3
HO
C C N
SH
H
NCC
O H
CH2
H
C C
OH
CH2
H
NN C C
H O
CH3 CH2CH2SCH3
H O
CCN
H
C C
OH
H
N
H
C C
OH
CH(CH3)2
N
HH
N
CH3
H O
CC
S
H
CC
O H
CH2OH
H
N CC
HO
CH3
CC
O H
H
N
H
CC
O H
CH(CH3)2
N
H H
N
CH3
HO
C C N
S
H
NCC
O H
CH2
H
[O]
Sanger’s Reagent: N-terminal Amino Acid Analysis
S G MVFA
Sanger's Reagent(2,4-dinitrofluorobenzene)
C C
OH
CH2OH
H
NH3N C C
H O
CH3 CH2CH2SCH3
H O
CC ON
H
C C
OH
H
N
H
C C
OH
CH(CH3)2
N
HH
N
CH2
H O
CC
C C
OH
CH2OH
H
N
H
N C C
H O
CH3
O2N
NO2
CH2CH2SCH3
H O
CC OHN
H
C C
OH
H
N
H
C C
OH
CH(CH3)2
N
HH
N
CH2
H O
CC
Sanger’s Reagent, cont’d
S
H3O, heat(total hydrolysis)
C C
OH
CH2OH
H
N
H
N C C
H O
CH3
O2N
NO2
CH2CH2SCH3
H O
CC OHN
H
C C
OH
H
N
H
C C
OH
CH(CH3)2
N
HH
N
CH2
H O
CC
C CO
OH
CH2OH
N N
CH2
H O
COC C CO
OH
CH(CH3)2
N C CO
OH
H
N
CH2CH2SCH3
H O
COCNH3H3H3 H3 H3
+
++ + +
"tagged" A
F V G M
) S, F, V, G, and M("tagged" A plus an equimolar mixture of
H
N C C
H O
CH3
O2N
NO2
OH
Carboxypeptidase: C-terminal AA Analysis
A F V MG
C C
OH
CH2OH
H
NH3N C C
H O
CH3 CH2CH2SCH3
H O
CC ON
H
C C
OH
H
N
H
C C
OH
CH(CH3)2
N
HH
N
CH2
H O
CC
C CO
OH
H
N
CH2CH2SCH3
H O
COCNH3
H3
+
S
G
M
Carboxypeptidase
C C
OH
CH2OH
H
NH3N C C
H O
CH3
C CO
OH
H
N
H
C C
OH
CH(CH3)2
N
HH
N
CH2
H O
CC
Carboxypeptidase
C C
OH
CH2OH
H
NH3N C C
H O
CH3
C CO
OH
CH(CH3)2
N
HH
N
CH2
H O
CC +
Prentice Hall c2002 Chapter 3 17
Acid-catalyzed hydrolysis of a peptide
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