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2016-11-06
1
Introduction to amino acids
and proteins
Amino Acids
• Amino Acids are the building units of proteins.
Proteins are polymers of amino acids linked
together by “ Peptide bond”.
2
Amino Acids
Each amino acid has 4 different groups attached
to α- carbon ( which is C-atom next to COOH).
3
R
αα
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Amino Acid Structure
• Amino acid carbons are named in sequence using the
Greek alphabet (α, β, γ, δ, ε) starting at the carbon
between the carboxyl and amino groups.
4
CH
COO
H 3 N
CH 2
CH 2
CH 2
CH 2
NH 3
αβγδε
Amino AcidsEach amino acid (except proline) has 4 groups:
� amino group,
�COOH group,
�Hydrogen atom
�and side Chain (R)
5
Amino AcidsAt physiological pH (7.4), the carboxyl group
(-COOH) is dissociated forming the negatively
charged carboxylate ion(-COO-), and the amino
group is protonated(-NH3+) forming positively
charged ion (NH3+) forming Zwitter ion
6
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Amino Acid Structure• Amino acids contain two functional groups,
a protonated amine and carboxylic acid in the form
of a carboxylate ion.
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• The side chain is unique for each amino acid.
Optical properties of amino acids
The α carbon of each amino acid is attached
to four different groups and is thus a chiral
or optically active carbon atom.
• When drawing the Fischer projection,
the carboxylate group is at the top of the structure
and the side chain (R group) is at the bottom.
• The protonated amine group can be on the left-hand
side (L form) or right-hand side (D form) of the
structure.
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L (S) –amino acid D (R)- amino acid
Optical properties of amino acids
• Amino acids with asymmetric centre at the α carbon can exist in two forms, L and D forms that are mirror images of each other and are called Enantiomers.
Optical properties of amino acids
The only amino acid not exhibiting chirality is
glycine. There are two hydrogen substituents
at the α-carbon, thus it is optically inactive.
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Stereochemistry of amino acids
• 19 of the 20 common amino acids have a chiral α-carbon atom (Gly does not)
• Threonine and isoleucine have 2 chiral carbons each (4 possible stereoisomers each)
• Mirror image pairs of amino acids are designated L (levo) and D (dextro)
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C COOH
H
NH2
CCH2
CH3
H
CH3**
isoleucine
C COOH
H
NH2
CCH3
OH
H
**
threonine
Threonine and isoleucine have 2 chiral carbons
Optical properties of amino acids
• All amino acids found in proteins are of
L-configuration
• D-amino acids occur in nature, but not in
proteins.
• D- amino acids are found in some
antibiotics and in bacterial cell walls.
Classification of amino acids
�Amino acids can be classified in 4 ways:
1. Based on structure
2. Based on the side chain characters
3. Based on nutritional requirements
4. Based on metabolic fate
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They are classified in three broad categories:
I. Mono amino mono carboxylic acid
(further subdivided in 5 groups):
1. Simple amino acids: glycine, alanine
2. Branched chain amino acids: valine,leucine,isoleucine
3. Hydroxyl group containing amino acids: serine, threonine
4. Sulphur containing amino acids: cysteine, methionine
5. Amide group containing amino acids: asparagine, glutamine
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Aliphatic Amino Acids:
1. Classification based on structure
They are classified in three broad categories:
II. Mono amino dicarboxylic acid
Example: aspartic acid, glutamic acid
III. Di /poly amino mono carboxylic acid
Example: lysine, arginine
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Aliphatic Amino Acids:
Aromatic Amino Acids:
Phenylalamime, tyrosine, tryptophan, histidine,
proline
Aliphatic Amino Acids
Glycine (Gly, G) Alanine (Ala, A) Valine (Val, V)
Leucine (Leu, L) Isoleucine (Ile, I)
Branched chain amino acids:
Valine, Leucine and Isoleucine
Valine R= isopropyl group
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Aliphatic Amino Acids
Branched chain amino acids:
R is isobutyl in both leucine and isoleucine but
branching is different:
• in leucine → branching occurs on γ carbon
• in isoleucine→ branching occurs on β- carbon19
Leucine (Leu, L) Isoleucine (Ile, I)
Neutral, hydroxy amino acids (-OH group-containing
amino acids): Serine and Threonine
Serine (Ser, S) Threonine (Thr, T)
Aliphatic Amino Acids
Sulfur-containing amino acids:Cysteine and Methionine
Aliphatic Amino Acids
Cysteine (Cys, C) Methionine (Met, M)
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Amide group-containing amino acids:
Asparagine and Glutamine
Aliphatic Amino Acids
Asparagine (Asn, N) Glutamine (Gln, Q)
Mono-amino di-carboxylic acids:
Aspartic acid and Glutamic acid
Aliphatic Amino Acids
Aspartate (Asp, D) Glutamate (Glu, E)
Di-/Poly- amino mono-carboxylic acids:
Lysine and Arginine
Aliphatic Amino Acids
Lysine (Lys, K) Arginine (Arg, R)
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Heterocyclic Amino Acids: Phenylalanine and tyrosine
Aromatic Amino Acids
Phenylalanine (Phe, F) Tyrosine (Tyr, Y)
Heterocyclic Amino Acids: Tryptophan and Histidine
Aromatic Amino Acids
Tryptophan (Trp, W) Histidine (His, H)
Imino acid- Proline
In proline, amino group enters in the ring formation being
α-imino group so proline is an α-imino acid rather than α-amino acid
Aromatic Amino Acids
Proline (Pro, P)
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Special groups in amino acids
� Arginine- Guanidinium group
� Phenyl Alanine- Benzene group
� Tyrosine- Phenol group
� Tryptophan- Indole group
� Histidine- Imidazole group
� Proline- Pyrrolidine
Proline has a secondary amino group, hence
it is an imino acid.
Special groups in amino acids
� Arginine- Guanidinium group
� Phenylalanine- Benzene group
� Tyrosine- Phenol group
Special groups in amino acids
� Tryptophan- Indole group
� Histidine- Imidazole group
12
4
3
5
Histidine
Indole
Imidazole
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Special groups in amino acids
� Proline- Pyrrolidine
Proline has a secondary amino group, hence
it is an imino acid.
Pyrrolidine Proline
32
2. Classification based on side chain characters
Nonpolar R = H, CH3, alkyl groups, aromatic ringsO
Polar ll
R = –OH, –SH, –C–NH2,
(polar groups with –O-, -SH, -N-)
Polar/Acidic
R = -COOH
Polar/ Basic
R = –NH2
2. Classification based on side chain characters
Amino acids with a non-polar side-chain:
e.g.: Glycine, Alanine, Valine, Leucine, Isoleucine,
Methionine, Phenylalanine, Tryptophan, Proline
• Each of these amino acids has a side chain that
does not bind or give off protons or participates
in hydrogen or ionic bonds.
• Side chains of these amino acids can be thought
of as “Oily” or lipid like, a property that promotes
hydrophobic interactions.
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34
2. Classification based on side chain characters
Amino acids with a polar but uncharged side-
chain:
Serine, Threonine, Tyrosine, Cysteine,
Asparagine and Glutamine
These amino acids are uncharged at neutral pH,
although the side chains of Cysteine and
Tyrosine can lose a proton at an alkaline pH.
2. Classification based on side chain characters
Amino acids with a polar but uncharged side-
chain
• Serine , Threonine and Tyrosine each contains
a polar hydroxyl group that can participate in
hydrogen bond formation.
• Side chains of Asparagine and Glutamine
contain a carbonyl group and amide group,
they can also participate in hydrogen bond
formation.
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Amino acids with a polar but uncharged side chain
37
2. Classification based on side chain characters
Amino acids with a charged polar side-chain
a) Amino acids with a positively charged side-chain:
The basic amino acids- Lysine, Arginine and
Histidine
b) Amino acids with a negatively charged side-chain:
The acidic amino acids- Glutamic acid and Aspartic
acid
They are hydrophilic in nature.
39
Amino acids with a charged side-chain
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40
Test – example 1
Identify each as (1) polar or (2) nonpolar
A. NH2–CH2–COOH (Glycine)
OH|
CH 2|
B. NH2–CH–COOH (Serine)
I. Essential amino acids:
These amino acids cannot be synthesized in
the body and have to be present essentially in
the diet.
Phenylalanine, Isoleucine, Leucine, Lysine,
Methionine, Threonine, Tryptophan and
Valine
FIL2M T2V
3. Classification based on nutritional requirements
II. Semi-essential amino acids:
These amino acids can be synthesized in the
body but the rate of synthesis is lesser than
the requirement(e.g. during growth, repair or
pregnancy) Arginine and Histidine
3. Classification based on nutritional requirements
(Arg & His)
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Alanine
Asparagine
Aspartic Acid
Cysteine
Glutamic acid
Glutamine
Glycine
Proline
Serine
Tyrosine
III. Non-essential amino acids:
These amino acids are
synthesized in the body,
thus their absence in the
diet does not adversely
affect the growth.
3. Classification based on nutritional requirements
1- Purely Ketogenic:
Leucine and Lysine are purely ketogenic because it will enter into the metabolic pathway of ketogenesis.
2- Ketogenic and Glucogenic:
Isoleucine, Phenylalanine, Tyrosine and Tryptophan
During metabolism, part of the carbon skeleton of these amino acids will enter the fatty acid metabolic pathway and
the other part into glucose pathway.
3- Purely Glucogenic:
All the remaining 14 amino acids are purely glucogenic as they enter only into the glucogenic pathway.
4. Classification based on on metabolic fate
The carbon skeleton of amino acids can be used either
for glucose production or for the production of ketone
bodies, based on that:
4. Classification based on on metabolic fate
Purely Glucogenic
amino acids
Purely
Ketogenic
amino acids
Both glucogenic
and ketogenic
amino acids
Glycine, Alanine,Arginine
Aspargine, Aspartic acid
Cysteine,
Glutamine, Glutamic acid
Histidine, Proline,
Methionine, Serine
Threonine, Valine
Leucine and
Lysine
Isoleucine,
Tyrosine,
Phenylalanine,
Tryptophan
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Fates of carbon
skeleton of amino
acids
Naming of Amino acids
Each amino acid has three letter (code) and
one letter (Symbol) abbreviations-
1) Unique first letter
• Cysteine- Cys- C
• Histidine- His- H
2) Priority of commonly occurring amino acids
• Alanine- Ala- A (Preference over Aspartate)
• Glycine- Gly-G (Preference over Glutamate)
Naming of Amino acids
3) Similar sounding names- Some one letter
symbols sound like the amino acids
• Tryptophan – W (Twyptophan)
• Phenylalanine – F
4) Letters close to initial letter
• Aspartate- Asx- B (near A)
• Lysine Lys- K (near L)
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Amino acid abbreviations
49
Properties of amino acids
Physical properties
• Colorless, form white crystals
• High melting point (More than 2000C)
Solubility
Most of amino acids are soluble in water, acids,
alkalis but insoluble in organic solvents.
Cysteine, aromatic and acidic amino acids are
slightly soluble in water.
Properties of amino acids
Taste Amino acids are:
� tasteless (e.g. Leucine, Lys, Trp, Asp, Cys),
� sweet (e.g. Gly, Ala, Val, Ser),
� bitter (Arginine, Isoleucine, Tyr, Ile, Leu)
If amino acids change their D-L configuration, in
general their taste is changing as well.
• Aspartame - An artificial sweetener contains
Aspartic acid and Phenylalanine.
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Properties of amino acids
Smell
• Most of amino acids are odorless, except for:
Cysteine and Methionine (an odour of sulfur
derivatives);
• Glutamic acid (a flavour of a broth,
it is broadly used in Chinese cousine,
enhances taste and smell of meals).
• A flavour of a bread comes from products of a
reaction of proline with glucose.
Isoelectric point
• Amino acids can exist as ampholytes or
zwitterions in solution, depending upon pH of
the medium.
• The pH at which the amino acids exist as
zwitterions, with no net charge on them is called
Isoelectric pH or Isoelectric point.
• In acidic medium, the amino acids exist as
cations
• In alkaline medium, they exist as anions.
Isoelectric point
CH COOHR
NH3+
CH COO - R
NH3+
zwitterionic form
NEUTRAL SOLUTION
pH = pI
CH COO - R
NH2
anionic form
negative ion
BASIC SOLUTION
pH greater than pI
cationic form
positive ion
ACIDIC SOLUTION
pH lower than pI
H+OH-
pH 13 Net charge -1 pH 7 Net charge 0 pH 1 Net charge +1
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Isoelectric point
Due to no net charge, there is no
electrophoretic mobility at Isoelectric pH.
Solubility and buffering capacity are also
minimum at Isoelectric pH
56
Isoelectric point
Amino Acids as Acids and Bases
Isoelectric point
Amino Acids as Acids and Bases
• Ionization of the –NH 2 and the –COOH group• Zwitterion has both a + and – charge• Zwitterion is neutral overall
NH2–CH2–COOH H3N+–CH2–COO–
glycine Zwitterion/dipolar ionof glycine
57
Test – example 2
CH3 CH3
+
H3N–CH–COOH H2N–CH2–COO–
(1) (2)
Select from the above structures
A. Alanine in base.
B. Alanine in acid.
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1) Strecker Synthesis
SYNTHESIS OF AMINO ACIDS
The Strecker Synthesis is a preparation of
α-aminonitriles, which are intermediates for the
synthesis of amino acids via hydrolysis of the nitrile.
58
CH3 CH2 COOH
propionic acid
1. Br2, PBr3
2. H2OCH33
CH2
COOH1
Br
NH3 excessCH33
CH2
COOH1
NH2
2-bromopropionic acid 2-aminopropionic acid
D-Alanine and L-Alanine
(1:1)
2) Bromination of a carboxylic acid
SYNTHESIS OF AMINO ACIDS
The bromoacid are conveniently prepared from
carboxylic acids by reaction with PBr3 .
Amination of alpha-bromocarboxylic acids provides a
straight forward method for preparing alpha-
aminocarboxylic acids.
Hell-Volhard-Zelinsky Reaction
59
NaBH4
CH33
CH2
COOH1
NH2
2-aminopropionic acid
D-Alanine and L-Alanine (1:1)
CH3 C COOH
O
pyruvic acid
(and alpha- keto acid)
NH3
3) Reductive amination of α-keto acids
SYNTHESIS OF AMINO ACIDS
60
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CH
NH2
CO
OHCH2CH2C
OH
O
+ NaOH + H2OCH
NH2
CO
OHCH2CH2C
O
O
Na
sodium glutamate
(main ingredient of Vegeta)
1) Amino acids are ampholytes - they can act as
either an acid or a base
reaction with a base (reaction of acidic –COOH
group)
Reactions of AA
sodium glutamate
(main ingredient of Vegeta)
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CH2
NH2
CO
OH + HCl CH2
NH3+
CO
OH
ammonium salt of GlycineCl-
reaction with an acid (reaction of basic –NH2 group)
Reactions of AA
62
CH2
NH2
CO
OH + CH2
NH2
CO
O CH2 CH3
C2H5HO
ester bond
+ H2O
ethyl ester of Glycine
conc. H2SO4
2) esterification reaction (reaction of –COOH group)
Reactions of AA
63
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CH3 CH COOH
NH2
Alanine
+ HNO2 CH3 CH COOH
OH+ N2 + H2O
an amino acid a hydroxy acid
Lactic acid
* *
3) dezamination of amino acids (reaction of –NH2 group) –
reaction with nitrous acid
Reactions of AA
64
65
4) decarboxylation reaction (reaction of –COOH group) –
for neutral and basic amino acids
CH2 CH COOH
NH2NH
N
*
histaminehistidine
CH2 CH2
NH2NH
N
+ CO2
Reactions of AA
CH22
C1
CH23
CH24
O
OHN
H H
C
NH
CH22
CH23
CH24
O
+ H2O
gamma-Lactam
(a cyclic amide)
alpha betagamma
NHO
5) condensation reaction of (gamma) γ-amino acids (reaction between –NH2 and –COOH of the same molecule)
Lactam rings are found in antibiotics’ molecules ( i.e. in penicillin).
Reactions of AA
66
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6767
6) acylation reaction (reaction of –NH2 group)
C
O
NH2CH2
OH+ CH3 C
Cl
O CH3 CO
C
O
NHCH2
OH + ClH
acethyl chlorideN-acethylglycine
Reactions of AA
6868
The Ninhydrin Reaction
In addition to these common reactions of amines and
carboxylic acids, common alpha-amino acids, except
proline, undergo a unique reaction with the
triketohydrindene hydrate known as ninhydrin.
Among the products of this unusual reaction is a purple
colored imino derivative, which provides as a useful
color test for amino acids, most of which are colorless. A
common application of the ninhydrin test is the
visualization of amino acids in paper chromatography.
Color reactions of amino acids
6969
Color reactions of amino acids