Chemistry of Proteins (Part I) / Chemistry of amino acids for medical, dental, nursing, Paramedical students.

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Protein Chemistry
Ashok Katta
Chemistry of Amino Acids
(Part – 1)

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Ashok KattaChemistry of amino acids
What are proteins?
Proteins are the most abundant and functionally
diverse molecules in living systems.
Every life process depends on this class of molecules
(proteins).
i.e proteins forms the fundamental basis of
structure and function of the life.
But how it possible……?

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Ashok KattaChemistry of Amino acids
Enzymes & polypeptide hormones
direct & regulate metabolism in the body.
In the bloodstream, proteins, such as
hemoglobin and plasma albumin, shuttle
molecules essential to life.
Contractile proteins in muscle permit
movement.
In bone, the protein collagen forms a
framework for the deposition of calcium
phosphate crystals
In short, proteins display an incredible diversity of functions, yet all share
the common structural feature of being linear polymers of amino acids.

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Ashok KattaChemistry of amino acids
Proteins are made up of what?
Proteins are the polymers of L-α- amino acids.
i.e proteins are made up of L-α- amino acids.

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Ashok KattaChemistry of amino acids
Then, What are Amino acids?
Amino acids are the group of compounds which
contains……
• An amino group (-NH2) and
• Carboxylic group (-COOH).

6. COO
-
R group
Amino group
Carboxylic group
Structure L-α-Amino Acid
a
H = Glycine
CH3 = Alanine
H N3
+ H

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Ashok KattaChemistry of amino acids
Standard Amino Acids
About 300 amino acids are found in the nature.
Of these only 20 amino acids are participate in the
protein biosynthesis.
And these 20 amino acids are called as Standard
amino acids.

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Ashok KattaChemistry of amino acids

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Ashok KattaChemistry of amino acids

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Ashok KattaChemistry of amino acids
Classification of Amino acids
There are four different ways of classification
of amino acids depending on………
Structure of amino acid
Nature of polarity
Nutritional requirement
Metabolic fate.

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Ashok KattaChemistry of amino acids
Classification of Amino acids
based on Structure
Based on chemical nature & Structure, amino
acids are classified as…
Aliphatic amino acids
Hydroxyl amino acids
Sulphur containing amino acids
Acidic amino acids and their amides
Basic amino acids
Aromatic amino acids
Imino acid

12. Leu L
-C-C-CONH2-C-CONH2
-C-COOH -C-C-COOH
-H -CH3
-C-OH -C-SH
-C-C-S-C
PPro
-C-C C
N N+
-C-C-C-C-NH3
+
-C-
-C- -OH
-C-
N
South line/
Hydroxyl & Sulfur AA
Circular line/
Imino acid
Central line/
Aliphatic AA
Northeast line/
Acidic AA &
their amides
North line/
Aromatic AA
Northwest line/
Basic AA
Amide
Acidic
-C-C-C-N-C-N
N+
=
C
-C-C-C
C
-C-C-C
C C
-C
C
C C
HN C-COOH
a-C-C
OH
Gln QAsn N
Asp D Glu EPhe F
Arg R
Lys K
His H
Gly G AAAla VVal IIle
YTyr
Ser S
Thr T Met M
Cys C
Amino Acid Subway Map
Trp W
Non-polar
Polar
This is NOT a metabolic pathway

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Ashok KattaChemistry of amino acids
Classification of Amino acids
based on Polarity
Based on Polarity of R
group, amino acids are
classified as…
Non polar amino acids:
R is hydrophobic group
which can’t enter in
hydrogen bond formation.
They don’t have charge on
R group.
following are the
example of non polar
amino acids
alanine,
valine,
leucine,
isoleucine,
phenylalanine,
tryptophan,
proline and
methionine

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Ashok KattaChemistry of amino acids
Classification of Amino acids
based on Polarity cont……
Polar amino acids with no
charge on R group:
R contains polar hydrophilic
group so can forms H bond
with H2O.
In those amino acids, R
may contain:
OH group : as in serine,
threonine and tyrosine
SH group : as in cysteine
amide group: as in glutamine
and aspargine.
Polar amino acids with +ve
charge on R group:
NH2 group or nitrogen act
as a base (basic AA): as
lysine, arginine and
histidine.
Polar amino acids with -ve
charge on R group:
COOH group (acidic amino
acids): as aspartic and
glutamic acid.

15. POLAR
NON-
POLAR
Tyr His
Gly
Acidic Neutral Basic
Asp
Glu Gln
Cys
Asn Ser
Thr Lys
Arg
Ala
Val
Ile
Leu Met
Phe Trp
Pro
Classification of Amino Acids by Polarity
Polar or non-polar, it is the bases of the amino acid properties.

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Ashok KattaChemistry of amino acids
Nutritional classification of Amino acids
All the 20 AA are required for the synthesis of proteins in the
body.
So, these AA has to supply in the diet.
Based on nutritional requirement in diet, these AA are
classified into….
Essential AA- the AAs which can not be synthesized by body, &
hence they have to supply in the diet. Their deficiency affects
growth, health and protein synthesis.
Semi essential AA- Out of ten essential AA namely Arginine &
Histidine can be synthesized by adults (but not by children).
Non essential AA – body synthesizes remaining 10 AA. So, these
are called as non essential AA.

17. EssentialAA
Non-
essential
Arg
Gly
Asp Glu GlnCys
Asn Ser
Thr
Lys
Ala
Val
Ile Leu
Met
Phe
Trp
Pro
Nutritional classification of Amino acids
H. VITTAL, LMP
Tyr
His

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Ashok KattaChemistry of amino acids
Classification of Amino acids
based on Metabolic fate
According to metabolic or degradation products of amino acids
they may be:
– Ketogenic amino acids: which give ketone bodies . Lysine and
Leucine are the only pure ketogenic amino acids.
– Both ketogenic and glucogenic amino acids: which give both
ketonbodies and glucose.These are: isoleucine, phenyl alanine,
tyrosine and tryptophan.
– Glucogenic amino acids: Which give glucose. They include the rest
of amino acids. These amino acids by catabolism yields products
that enter in glycogen and glucose formation.

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Ashok KattaChemistry of amino acids
Properties of Amino acids
Amphoteric properties of amino acids:
– Amino acids have both basic and acidic groups.
– So, they can donate proton and accept proton. act as
base or acid.

20. HighLow
Proton： abundant and small, affects the charge of a molecule
H+
lone pair
electrons
H
H
H+
NH
H
NAmino
H+
Ampholyte contains both positive and negative groups on its molecule
Carboxylic C
O
O
H
C
O
O
Proton Is Adsorbed or Desorbed
pKa
LowHigh pKa

21. COO
-
R
Optical Isomers Of Amino Acids
aH N3
+
H
COO-
R
a H N3
+
H
L-Amino acid D-Amino acid

22. Mirror Images of Amino Acid
a aMirror
image
Same chemical properties
Stereo isomers

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Ashok KattaChemistry of amino acids
Zwitter ion or dipolar ion:
– Meaning of Zwitter ion is a hybrid molecule which
carries both +ve and –ve charge.
– Depending on the pH of the medium amino acid
either carry +ve charge or –ve.
– Each AA has a characteristic pH at which it carry
both charges and exist as Zwitter ion.
– Example-leucine, pH-6.0

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Ashok KattaChemistry of amino acids
Isoelectic pH (pl)
It is the pH at which a molecule exist as a
zwitterion.
At pl molecule carry no net charge.
Thus, the molecule is electrically neutral.

25. COOH
NH2 H+
COO-
R-C-H
NH2 H+
R-C-H
COO-
NH2
R-C-H
Acidic environment Neutral environment Alkaline environment
+1 -10
pK1 ~ 2
pK2 ~ 9
Isoelectric point
5.5

26. 12
9
6
3
0
[OH] →
★
★
pK1
pK2
pH
pIH-C-R
COO-
NH2 H+
Isoelectric point =
pK1 + pK2
2
Amino Acids Have Buffering Effect

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Ashok KattaChemistry of amino acids
Reactions due to COOH group:
– Salt formation- AA forms salts with alkalis,
– Amide formation- AA forms amide with ammonia and
– Amine formation- AA undergo decarboxylation to
produce corresponding amines.
• Example: histamine, tyramine & GABA from histidine,
tyrosine & glutamate resp.

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Ashok KattaChemistry of amino acids
Reactions due to NH2 group:
– Amino group of AA react with acids to give salt.
– Reaction with Ninhydrin:
• amino group of α-amino acid reacts with ninhydrin
solution yielding intense blue/ purple colored product.
• intense blue/ purple color is called Ruhemann’s purple.
• But proline and hydroxyproline give yellow color with
ninhydrine.
Ruhemann’s purple
Amino acid + Ninhydrin Keto acid + NH3 + CO2 + Hydrindantin
Hydrindantin + NH3 + Ninhydrin

29. NH2 COOH1 NH2 COOH2
NH2 C N COOH
O
H
21
Amino acids are connected head to tail
Formation of Peptide Bonds
Dehydration
H2O

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Ashok KattaChemistry of amino acids
Peptide formation
The most important reaction of AA is peptide bond
formation.
Peptides are polymer of AAs.
2 AAs are covalently linked with each other by
peptide bond to gives rises to dipeptide.
Similarly when 3 AAs are linked by peptide bond to
give tripeptide and so on…
When many AAs are joined the product is called
polypeptide.
Proteins are the polypeptide with thousands of AAs.

31. NH2 COOH1 NH2 COOH2
NH2 C N COOH
O
H
21
Formation of polypeptide
Dehydration
H2O
NH2 COOH3
NH2 C N C
O
H
21 N COOH3
O
H
H2O

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Ashok KattaChemistry of Amino acids
Colour reactions of Amino acids
Amino acids can be identified by specific Colour reactions
.
Reaction Specific group or amino acid
1. Biuret reaction Two peptide linkages
2. Ninhydrin reaction α-amino acids
3. Xanthoproteic reaction Benzene ring of aromatic a.as.
4. Millons reaction Phenolic group (Tyr)
5. Hopkins – Cole reaction Indole ring (Trp)
6. Sakaguchi reaction Guanidino group (Arg)
7. Nitroprusside reaction Sulfhydryl groups ( Cys)
8. Sulfur test Sulfhydryll groups ( Cys)
9. Pauly’s test Imidazole ring ( His)

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Ashok KattaChemistry of amino acids
Generally, the term peptide is applied when the no. of
AAs is less than 10.
Some examples of biologically important peptides and
their functions are……
– Glutathione
– Thyrotropin releasing hormone (TRH) (tripeptide)
– Oxytocin (9 AAs)
– Vasopressin (9 AAs)
– Gastrin
– Angiotensin
– Bradykinin
– Peptide antiboitics

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Ashok KattaChemistry of amino acids
It is tripeptide.
Chemically it is γ- glutamyl-cysteinyl-glycine.
It exists in two forms – reduced and oxidized.
Functions-
It serves as redox buffer regulating the redox state of
the cell
It prevent the oxidation of (-SH) gr of proteins.
It plays a key role in detoxification of H2O2.
It is involved in transport of AA in kidney and intestine.
It requires to maintain normal structure of RBC cell
membrane and to keep Hb in the ferrous state.
G-SH G-S-S-G
reduced glutathione Oxidized glutathione
Glutathione

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Ashok KattaChemistry of amino acids
Apart from these 20 AA, there are several
other AA which are biologically important.
These includes……
– Amino acid derivatives
– Non-protein Aas and
– D-amino acids.

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Ashok KattaChemistry of amino acids
Amino acid derivatives
– These are synthesized by post transcriptional
modification of the 20 SAAs.
– These derivatives of AAs are very important for
protein structure & functions.
– Examples are……
• 4-hydroxyproleine and 5-hydroxylysine (Collagen)
• γ-carboxyglutamic acid (coagulation proteins)
• Methylated, phosphorylated and acetylated AA
(Histones)
• Cystine- combination of two cysteines.

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Ashok KattaChemistry of amino acids
Non-protein amino acids:
– These AAs never found in the protein structure
but perform several biological functions.
– These are……
• Ornithine
• Citrulline
• Arginosuccinic acid
• Thyroxine
• Triiodothyronine
• S-adenosylmethionine
• Homocysteine
• DOPA
• Creatinine
• β-Alanine
• γ-aminobutyric acid

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Ashok KattaChemistry of amino acids
Formation of proteins
Formation of glucose
Enzyme activity
Transport & storage form of ammonia (Glutamine)
As a buffer
Detoxification reactions
Formation of Biologically importance compounds.
Useful as drugs- (non standard AAs)
– D-Pencillamine (D-dimethylglycine) – Wilson’s disease.
– N-Acetylcysteine – in cystic fibrosis, CRF.

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E mail –
For more presentation visit -
Ashok Katta
Dept. of Biochemistry,
Dhanalakshmi Srinivasan Medical College,
Perambalur
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