Amino Acids and ProteinsAmino Acids and Proteins
• Proteins are composed of amino acids.
• There are 20 amino acids commonly found in proteins. All have:
Cαα
H
COOHNH2
R
Amino acids at neutral pH are dipolar ions (zwitterions) because their αα-carboxyl and αα-amino groups are ionized.
C COONH3
H
R
+
[NaOH][NaOH]0. 50. 5
22
44
66
88
pK1pK1
pK2pK2
Titration curve for Glycine:Titration curve for Glycine:
pHpH COOH=COO-COOH=COO-
NH3+
NH2
NH3+ =NH2
[NaOH][NaOH]0. 50. 5
22
44
66
88
pK1pK1
pK2pK2
pHpHCOOHCOOH
NH3+NH3+
[NaOH][NaOH]0. 50. 5
22
44
66
88
pK1pK1
pK2pK2
pHpHCOOHCOOH
NH3+NH3+
Isoelectric point (no net charge)
Isoelectric point (no net charge)
pKa Values of the Amino Acids
You should know these numbers and knowwhat they mean!
• Alpha carboxyl group - pKa = 2
• Alpha amino group - pKa = 9
• These numbers are approximate, butentirely suitable for our purposes.
COO-
- C -H3+N H
CH3CH3
COO-
- C -H3+N H
CH2CH2
CHCHCH3CH3 CH3CH3
COO-
- C -H3+N H
H C H - C -
CH3CH3
CH2CH2
CH3CH3
Aliphatic Non-Polar Amino Acids
Alanine (Ala, A)
COO-
- C -H3+N H
CHCHCH3CH3 CH3CH3
Valine (Val, V)
Leucine (Leu, L) Isoleucine (Ile, I)
CH2
+N
COO-
H2C H2C CH2CH2
CH2CH2H
Proline (Pro, P) COO-
- C -H3+N H
CH2CH2
SS
CH3CH3
CH2CH2
Methionine (Met, M)
Aromatic Non-Polar Amino Acids
COO-
- C -H3+N H
CH2CH2
Phenylalanine (Phe, F)
COO-
- C -H3+N H
CH2CH2
CHCHCC
NN
Tryptophan (Trp, W)HH
Polar Uncharged Amino AcidsPolar Uncharged Amino AcidsCOO-
- C -H3+N H
CH2OHCH2OH
Serine (Ser, S)CH3CH3
COO-
- C -H3+N H
CHOHCHOH
Threonine (Thr, T)
COO-
- C -H3+N H
CH2CH2
SHSH
Cysteine (Cys, C)
COO-
- C -H3+N H
HH
Glycine (Gly, G)
Tyrosine (Tyr, Y)
COO-
- C -H3+N H
CH2CH2
OHOH
pKa=13pKa=13
pKa=10.1 pKa=8.3
Polar Uncharged Amino AcidsPolar Uncharged Amino Acids
COO-
- C -H3+N H
CH2CH2
CCOO NH2NH2
CH2CH2
Glutamine (Gln, Q)
COO-
- C -H3+N H
CH2CH2
CCOO NH2NH2
Asparagine (Asn, N)
Acidic Amino AcidsAcidic Amino Acids
COO-
- C -H3+N H
CH2CH2
CCOO
Aspartate (Asp, D)
O-O-
COO-
- C -H3+N H
CH2CH2
CCOO
CH2CH2
Glutamate (Glu, E)
O-O-
pKa=3.9pKa=4.3
Basic Amino AcidsBasic Amino Acids
CH2CH2
COO-
- C -H3+N H
NH3+NH3+
CH2CH2
CH2CH2
CH2CH2
Lysine (Lys, K)
COO-
- C -H3+N H
H2+NH2+N NH2
NH2
CH2CH2
CH2CH2
CH2CH2
NHNH
CC
Arginine (Arg, R)
COO-
- C -H3+N H
NN
CH2CH2
CC
NHNHCCHH
HCHC=
Histidine (His, H)
pKa=10.5pKa=12.5
pKa=6.0
COO-
- C -H3+N H
CH2OHCH2OH
serine
CH3CH3
COO-
- C -H3+N H
CHOHCHOH
threonine
COO-
- C -H3+N H
CH2OPO32-CH2OPO32-
phosphoserine
CH3CH3
COO-
- C -H3+N H
CHOPO32-CHOPO32-
phosphothreonine
Serine and Threonine can be PHOSPHORYLATED:Serine and Threonine can be PHOSPHORYLATED:
ATP ADP, Pi
ATP ADP, Pi
COO-
- C -H3+N H
CH2CH2
S S
COO-
- C -H3+N H
CH2CH2
SS
Disulfide Bond:Two cysteine 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 αα-keratin protein (that hair is made of) and spontaneous re-oxidation of those disulfide bonds in air.
Cystine
Uncommon Amino Acids
• Hydroxylysine, hydroxyproline - collagen
• Carboxyglutamate - blood-clotting proteins
• Pyroglutamate - bacteriorhodopsin
• Phosphorylated amino acids - signalingdevice
Titration of Glutamic Acid
Titration of Lysine
A Sample Calculation
What is the pH of a glutamic acid solution ifthe 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 sidechain 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 andamides
• Side chains show unique reactivities– Cys residues can form disulfides and can be
easily alkylated
– Few reactions are specific to a single kind ofside chain
Stereochemistry of Amino Acids
• All but glycine are chiral
• L-amino acids predominate in nature
• D,L-nomenclature is based on D- and L-glyceraldehyde
• R,S-nomenclature system is superior,since amino acids like isoleucine andthreonine (with two chiral centers) can benamed unambiguously
Spectroscopic Properties
• All amino acids absorb in infrared region
• Only Phe, Tyr, and Trp absorb UV
• Absorbance at 280 nm is a gooddiagnostic device for amino acids
• NMR spectra are characteristic of eachresidue in a protein, and high resolutionNMR measurements can be used toelucidate three-dimensional structures ofproteins
Separation of Amino Acids
• Mikhail Tswett, a Russian botanist, firstseparated colorful plant pigments by‘chromatography’
• Many chromatographic methods exist forseparation of amino acid mixtures– Ion exchange chromatography
– High-performance liquid chromatography
Top Related