amino acids
TRANSCRIPT
Amino acids Compiled and Edited by
Dr. Syed Ismail Associate Professor, SSAC
College of Agriculture, VN MKV Parbhani
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
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
4 Compiled & Edited by Dr Syed Ismail,
MKV Parbhani
Amino Acid Enantiomers
•Steroisomers / enantiomers
•Biological system only synthesize
and use L-amino-acids
5 Compiled & Edited by Dr Syed Ismail,
MKV Parbhani
Amino Acid Classification
• Aliphatic
• Aromatic
• Sulfur containing
• Polar/uncharged
• basic/acidic
Hydrophobic
Hydrophilic
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Ismail, MKV Parbhani
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Am
ino
Acid
Typ
es
Name R-Group Properties
Glycine G Gly Hydrophobic
Alanine A Ala Hydrophobic
Valine V Val Hydrophobic
Leucine L Leu Hydrophobic
Isoleucine I Ile Hydrophobic, two chiral carbons
Proline P Pro Cyclic, not terribly hydrophobic
Phenylalanine F Phe Hydrophobic, bulky
Tyrosine Y Tyr Less hydrophobic (than Phe), bulky
Tryptophan W Trp Hydrophobic, bulky (indole ring)
Cysteine C Cys Hydrophobic, highly reactive (S-S link)
Methionine M Met Hydrophobic (start a.a.)
Serine S Ser Hydrophilic, reactive
Threonine T Thr Hydrophilic, reactive, two chiral carbons
Lysine K Lys Highly hydrophilic, positively charged
Arginine R Arg Highly hydrophilic, positively charged
Histidine H His Highly hydrophilic, positive or neutral
Aspartate D Asp Highly hydrophilic, negatively charged
Glutamate E Glu Highly hydrophilic, negatively charged
Asparagine N Asn Uncharged
Glutamine Q Gln Uncharged
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
Hyd
rop
ho
bic
ity
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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 9
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.
10 Compiled & Edited by Dr Syed
Ismail, MKV Parbhani
• 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 –
Acidic Amino Acids
11 Compiled & Edited by Dr Syed Ismail,
MKV Parbhani
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
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Histidine Lysine Arginine
• 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
Polar Uncharged Amino Acids
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Ismail, MKV Parbhani
Essential/Non-Essential Amino Acids
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Ismail, MKV Parbhani
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-)
17 Compiled & Edited by Dr Syed Ismail,
MKV Parbhani
Peptide Ends are Not the Same Numbering starts from the amino terminus
AA1 AA2 AA3 AA4 AA5
18 Compiled & Edited by Dr Syed Ismail,
MKV Parbhani
Compiled & Edited by Dr Syed
Ismail, MKV Parbhani
19
Pro
tein
Pri
mary
Str
uctu
re
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)
Proteins are:
• Cofactor is a general term for functional non-amino acid component – Metal ions or organic molecules
• Coenzyme is used to designate an organic cofactors – NAD+ in lactate dehydrogenase
• Prosthetic groups are covalently attached cofactors – Heme in myoglobin
• Polypeptides (covalently linked -amino acids) + possibly –
• cofactors,
• coenzymes,
• prosthetic groups,
• other modifications
20 Compiled & Edited by Dr Syed
Ismail, VN MKV Parbhani
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
21 Compiled & Edited by Dr Syed
Ismail, MKV Parbhani
Compiled & Edited by Dr Syed
Ismail, MKV Parbhani
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Fiv
e C
ate
go
rie
s
Note 20
(naturally
translated)
amino acids