1. Amino acids
Compiled and Edited by
Dr. Syed Ismail
Associate Professor, SSAC
College of Agriculture, VN MKV Parbhani

2. Amino Acids: Building Blocks of Protein
1. Proteins are heteropolymers of -amino acids
2. Amino acids have properties that are well suited to carry out a
variety of biological functions
Functions:
1. Capacity to polymerize
2. Useful acid-base properties
3. Varied physical properties
4. Varied chemical functionalities

4. Most -Amino Acids are Chiral
 The -carbon has always four
substituents and is tetrahedral
 All (except proline) have an
acidic carboxyl group, a basic
amino group, and an alpha
hydrogen connected to the carbon
 Each amino acid has an
unique fourth substituent R
 In glycine, the fourth
substituent is also hydrogen
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Compiled & Edited by Dr Syed Ismail,
MKV Parbhani

5. Amino Acid Enantiomers
•Steroisomers / enantiomers
•Biological system only synthesize
and use L-amino-acids
Compiled & Edited by Dr Syed Ismail,
MKV Parbhani
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6. Amino Acid Classification
• Aliphatic
• Aromatic
• Sulfur containing
Hydrophobic
• Polar/uncharged
• basic/acidic
Hydrophilic
Compiled & Edited by Dr Syed
Ismail, MKV Parbhani
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7. Amino Acid Types
Name
Glycine
Alanine
Valine
Leucine
Isoleucine
Proline
Phenylalanine
Tyrosine
Tryptophan
Cysteine
Methionine
Serine
Threonine
Lysine
Arginine
Histidine
Aspartate
Glutamate
Asparagine
Glutamine
R-Group Properties
G
A
V
L
I
P
F
Y
W
C
M
S
T
K
R
H
D
E
N
Q
Gly
Ala
Val
Leu
Ile
Pro
Phe
Tyr
Trp
Cys
Met
Ser
Thr
Lys
Arg
His
Asp
Glu
Asn
Gln
Hydrophobic
Hydrophobic
Hydrophobic
Hydrophobic
Hydrophobic, two chiral carbons
Cyclic, not terribly hydrophobic
Hydrophobic, bulky
Less hydrophobic (than Phe), bulky
Hydrophobic, bulky (indole ring)
Hydrophobic, highly reactive (S-S link)
Hydrophobic (start a.a.)
Hydrophilic, reactive
Hydrophilic, reactive, two chiral carbons
Highly hydrophilic, positively charged
Highly hydrophilic, positively charged
Highly hydrophilic, positive or neutral
Highly hydrophilic, negatively charged
Highly hydrophilic, negatively charged
Uncharged
Uncharged
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8. Hydrophobicity
Aliphatic (alkane) Amino Acids
•Proline (pro, P)- cyclic “imino acid”
•Glycine(gly, G)-only non-chiral amino acid, not hydrophobic
•Alanine (ala, A) – R-group = methyl-group
•Valine (Val, V) –
•Leucine (Leu, L) –
•Isoleucine (Ile, I) -2 chiral carbons
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9. Aromatic Amino Acids
•
•
•
•
•
•
All are hydrophobic
All contain aromatic group
Absorb UV at 280 nm
Phenylalanine (Phe, F)
Tyrosine (Tyr, Y) – -OH ionizable (pKa = 10.5), H-Bonding
Tryptophan (Trp, W) – bicyclic indole ring, H-Bonding
Phe
Tyr
TRP
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10. Sulfur Containing Amino Acids
• Methionine (Met, M) – “start” amino
acid, very hydrophobic
• Cysteine (Cys, C) – sulfur in form of
sulfhydryl, important in disulfide
linkages, weak acid, can form
hydrogen bonds.
Compiled & Edited by Dr Syed
Ismail, MKV Parbhani
10

11. Acidic Amino Acids
• Contain carboxyl groups (weaker acids than a-carboxyl-group)
• Negatively charged at physiological pH, present as conjugate
bases (therefore –ate not –ic acids)
• Carboxyl groups function as nucleophiles in some enzymatic
reactions
• Aspartate –
• Glutamate –
Compiled & Edited by Dr Syed Ismail,
MKV Parbhani
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12. Basic Amino Acids
• Hydrophillic nitrogenous bases
• Positively charged at physiological pH
• Histidine – imidazole ring protonated/ionized, only amino acid
that functions as buffer in physiological pH range.
• Lysine - diamino acid, protonated at pH 7.0
• Arginine - guianidinium ion always protonated, most basic amino
acid
Histidine
Lysine
Arginine
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13. Polar Uncharged Amino Acids
• Polar side groups, hydrophillic in nature, can form hydrogen bonds
• Hydroxyls of Ser and Thr weakly ionizable
• Serine (Ser, S) – looks like Ala
• Threonine (Thr, T) – 2 chiral carbons
• Asparagine (Asn, N) – amide of aspartic acid
• Glutamine (Gln, Q) – amide of glutamic acid
Compiled & Edited by Dr Syed
Ismail, MKV Parbhani
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14. Essential/Non-Essential Amino Acids
Compiled & Edited by Dr Syed
Ismail, MKV Parbhani
14

17. Peptides and Peptide bonds
 Peptide bond in a
di-peptide
 “Peptides” are
small
condensation
products of amino
acids
 They are “small”
compared to
proteins (di, tri,
tetra… oligo-)
Compiled & Edited by Dr Syed Ismail,
MKV Parbhani
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18. Peptide Ends are Not the Same
Numbering starts from the amino terminus
AA1
AA2
AA3
AA4
Compiled & Edited by Dr Syed Ismail,
MKV Parbhani
AA5
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19. Protein Primary Structure
Note the
Polarity of
the
sequence
(amino 
carboxy)
Note also the disulfide
linkages (cys-cys  S-S
bonds; actually considered
a component of tertiary
structure)
Compiled & Edited by Dr Syed
Ismail, MKV Parbhani
19

20. Proteins are:
• Polypeptides (covalently linked -amino acids) + possibly –
• cofactors,
• coenzymes,
• prosthetic groups,
• other modifications
•
Cofactor is a general term for functional non-amino acid component
–
•
Coenzyme is used to designate an organic cofactors
–
•
Metal ions or organic molecules
NAD+ in lactate dehydrogenase
Prosthetic groups are covalently attached cofactors
–
Heme in myoglobin
Compiled & Edited by Dr Syed
Ismail, VN MKV Parbhani
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21. Protein Nomenclature
• Peptides 2 – 50 amino acids
• Proteins >50 amino acids
• Amino acid with free -amino group is the
amino-terminal or N-terminal residue
• Amino acid with free -carboxyl group is the
carboxyl-terminal or C-terminal residue
• Three letter code – Met-Gly-Glu-Thr-Arg-His
• Single letter code – M-G-E-T-R-H
Compiled & Edited by Dr Syed
Ismail, MKV Parbhani
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22. Five Categories
Note 20
(naturally
translated)
amino acids
Compiled & Edited by Dr Syed
Ismail, MKV Parbhani
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