Amino acids are the building blocks of proteins. They join together through peptide bonds to form polypeptide chains. There are over 300 amino acids described in nature but only 20 are commonly found in mammalian proteins. Amino acids have various roles including forming enzymes, hormones, antibodies and being precursors for other important molecules. They are also important for buffering pH changes and participating in metabolic reactions through side chain functional groups.

2. AMINOACID CHEMISTRY
BY
DR SHAMIM AKRAM
AP BIOCHEM AIMC

3. •CHEMISTRY OF AMINOACIDS
•BY
•DR SHAMIM AKRAM
•AP Biochem.AIMC

4. Amino Acids
•
•
•
Aminoacids are building blocks of proteins.Individual
Aminoacids are joined together through peptide linkage to
form polypeptide chains of proteins.
Proteins when hydrolyzed either by boiling with acids or
through the action of enzymes like trypsin, are broken down
into their component amino acids.
Although >300 different amino acids have been described in
nature, only 20 are commonly found as constituents of
mammalian proteins. [Note: These standard amino acids are
the only amino acids that are encoded by DNA.
Nonstandard amino acids are produced by chemical
modification of standard amino acids

5. WHAT DO AMINO ACIDS DO?
 Amino acids are essential to life, have a role in metabolism,
and are important in nutrition.
 They form short polymer chains called peptides, as well as longer chains that
are called polypeptides or proteins.
 About 75 percent of the human body is made up of chains of amino acids,
which is why they are so vital to how your system functions.
 All the chemical reactions that occur in the body depend on amino acids and
the proteins they build (Enzymes,Hormones,Neurotransmitters,Antibodies
etc.).

6. Functions of amino acids
 A variety of roles inmetabolism
 the building blocks of proteins
 forming parts of coenzymes e.g.SAM,Serine
 as precursors for the biosynthesis of molecules such as
heme,glutathion,pyruvate,OAA,Catecholamines,Melanine,
Niacin, Serotonine,Histamine,Creatine,NO,etc.
 Buffer action: mostly by histidine in Hb.

7. Buffer action of Hb is due to Histidine
• Amino acids with basic side chains
• The side chains of the basic amino acids accept protons . At physiologic pH,
the R groups of lysine and arginine are fully ionized and positively charged.
• In contrast, the free amino acid histidine is weakly basic and largely
uncharged at physiologic pH. However, when histidine is incorporated into
a protein, its R group can be either positively charged (protonated) or
neutral, depending on the ionic environment provided by the protein.
• This important property of histidine contributes to the buffering role it
plays in the functioning of such proteins as hemoglobin.
• [Note: Histidine is the only amino acid with a side chain that can ionize
within the physiologic pH range.]

8. Nutritional Value of Aminoacids
• Complete proteins/1st class proteins:
• These contain all essential amino acids in sufficient quanity.Examples
are meat,fish,poultry,dairy products(animal)
• Incomplete proteins/2nd class 1 proteins:
• These donot contain all essential amino acids in sufficient
quanity.Examples are pulses,legumins,soya(plant)
• Both can be combined to get sufficient amount of essential amino
acids.

9. General Structure of Amino Acids
• The amino group is
attached to the
α- carbon which is
next to the
carboxyl group;
hence the name
α-amino acid

12. Amino acids join together via peptide bonds
6
• Chain of amino acids = peptide or protein
Two amino acids can react with loss of a water molecule to form a covalent bond.
Amide linkage is planar NH
and CO are anti

13. PROPERTIES OF AMINO ACIDS
The amino acids differ in their physiochemical properties which determine the
characteristic of protein.
A. Physical properties
B. Chemical properties

14. PHYSICAL PROPERTIES OF AMINO ACIDS
 Colorless,
 crystals,
 soluble in water,
 insoluble in ether.
 D and L Isomers
 All amino acids( except glycine) are
optically active.
 Amphoteric (react as acidic and basic),
(NH2 and COOH group).
Understanding these physical properties, including charge, solubility
and pKa, aid in designing peptide sequences

15. PHYSICAL PROPERTIES
1.Solubility : Most of the amino acids are usually soluble in water and insoluble in
organic solvents.
2.Melting point : Amino acids generally melt at higher temperatures, often above
200°C.
3.Taste : Amino acids may be sweet (Gly,Ala, Val), tasteless (Leu) or bitter (Arg,
Ile), Monosodium glutamate (MSG; ajinomotto) is used as a flavouring agent in
food industry.

16. PHYSICAL PROPERTIES
4. Optical properties: All amino acids except glycine possess
optical isomers due to the presence of asymmetric carbon
atom. Some amino acids have a second asymmetric carbon
e.g. isoleucine, threonine

17. Amino acid isomers
• Because the α-carbon of an amino acid is attached to four different
chemical groups, it is an asymmetric (chiral) atom. Glycine is the
exception because its α-carbon has two hydrogen substituents.
• Amino acids with a chiral α- carbon exist in two different isomeric
forms, designated D and L, which are enantiomers, or mirror images.

18. ISOMERISM

19. 5. Amino acids as ampholytes : amino acid contains both acidic(-COOH) and
basic (-NH2) groups. They can donate a proton or accept a proton , hence amino
acids are regarded as ampholytes.

20. CONT……
…
6. Zwitterion or dipolar ion: it is a hybrid molecule containing positive and
negative groups. The amino acids rarely exist in a neutral form with free
carboxylic (-COOH) and free amino (-NH2) groups.
In strongly acidic pH(low pH), the amino acid is positively charged (cation)
while in strongly alkaline pH (high pH), it is negatively charged (anion). Each
amino acid has a characteristic pH (e.g. leucine, pH 6.0) at which it carries both
positive and negative charge and exist as a zwitter ion.

22. H
R-C-COO-
H
R-C-COOH
H
R-C-COO-
NH+
3
H
R-C-COOH
NH+
3
NH2
Amino acid
Cation
(low pH)
Zwitterion
(isoelectric pH)
H+
NH2
Anion
(high pH)
H+
H+
H+
EXISTENCE OF AMINO ACID AS CATION, ANION AND ZWITTERION

23. CONT……
…
8. Titration of amino acids: The existence of different ionic forms of amino acids
can be more easily understood by the titration curves.
Example: At low pH leucine exists as a fully protonated form as cation. As the
titration proceeds with NaOH, leucine loses its protons and at isoelectric pH, it
becomes a zwitterion. Further titration results in the formation of anionic form of
leucine.

25. CONT………
7. Isoelectric pH (symbol pI): the pH at which a molecule exists as a zwitter ion
and carries no net charge making the molecule electrically neutral.
The pI value can be calculated by taking the average pKa values
corresponding to the ionizable groups. For example: leucine has two ionizable
groups, and its pI can be calculated as follows.
3General formula- pK1(COO-) + pK2 (NH+ )
For leucine-
pH= ------------------------------
2
2.4+9.6
pI= ---------- = 6.0
2

28. CHEMICAL PROPERTIES

29. 1) Reactions due to amino group
29
2) Reactions due to carboxyl group
3) Reactions due to side chain
4) Reaction due to both amino and carboxyl groups

30. Formation of carbamino compound
CO2 binds to α amino acid on the globin chain of
hemoglobin to form carbamino hemoglobin
The reaction takes place at alkaline pH and serves as a
mechanism for the transfer of Carbon dioxide from the
tissues to the lungs by hemoglobin.
30

32. 1) Decarboxylation- Amino acids undergo
alpha decarboxylation to form
corresponding amines. Examples-
Glutamic acid
Histidine
Tyrosine
GABA
Histamine
Tyramine
2) Formation of amide linkage
• Non α carboxyl group of an acidic amino acid reacts
with ammonia by condensation reaction to form
corresponding amides
Aspartic acid
Glutamic acid
Asparagine
Glutamine
32

34. 1) Ester formation
34
 OH containing amino acids e.g. serine, threonine can
form esters with phosphoric acid in the formation of
phosphoproteins.
 OH group containing amino acid can also
form: Glycosides – by forming
 O- glycosidic bond with carbohydrate residues.

35. 2) Reactions due to SH group (Formation of disulphide
bonds)
Cysteine has a sulfhydryl group( SH) group and can form a
disulphide (S-S) bond with another cysteine residue.
 The dimer is called Cystine
Two cysteine residues can connect two polypeptide chains by
the formation of interchain disulphide chains.
7/5
35

36. 3)Transmethylation
The methyl group of Methionine can be transferred after activation to
an acceptor for the formation of important biological compounds.
36

37. 4)Reactions due to both amino & carboxyl groups
Formation of peptide bond
Reactions due to side chains
2
37

39. Reaction with ninhydrin
• The α- amino acids react with ninhydrin to form a purple, blue or
pink colour complex (Ruhemann’s purple).
•Amino acid + Ninhydrin ------> Keto acid + NH3 + CO2 +
Hydrindantin Hydrindantin + NH3 + Ninhydrin ------>
Ruhemann’spurple
• Ninhydrin’s reaction is effectively used for the quantitative
deamination of amino
acids and proteins. (Proline gives yellow colour with ninhydrin).

40. Colour reactions of amino acids
Amino acids can be identified by specific colour

41. S.No. Test Significance
1) Ninhydrin reaction Given by all Alpha amino acids
2) Xanthoproteic test Given by aromatic amino acids
3) Millon’s test Confirmatory test for Tyrosine
4) Biuret test Not given by free amino acids
5) Sakaguchi test Given by Arginine
6) Hopkins Cole reaction Confirmatory test for Tryptophan
7) Lead acetate test Given by cysteine and cystine but not given by
Methionine
8) Nitroprusside reaction Given by SH group containing amino acids
41

42. COLOUR REACTION OF AMINO ACIDS
SL.
NO.
REACTION SPECIFIC GROUP OR
AMINOACID
COLOUR
1. Xanthoproteic reaction Benzene ring of aromatic
amino acids (Phe, Try, Trp)
Yellow
2. Millons reaction Phenolic group (Tyr) Red
3. Hopkins-Cole reaction Indole ring (Trp) Purple
4. Sakaguchi reaction Gaunidino group (Arg) Red
5. Nitroprusside reaction Sulfhydryl group (Cys) Bright red
6. Pauly’s test Imidazole ring (His) Red

43. NOMENCLATURE OF A.A.
• One letter abbreviation
• or
• Three letter abbreviation
• e.g. for Alanine A or Ala

44. Amino Acids found in Proteins
Amino acids 1-Letter 3-letter
Abbreviation Abbreviation
Alanine A Ala
Arginine R Arg
Asparagine N Asn
Aspartic acid D Asp
Cysteine C Cys
Glutamine Q Gln
Glutamic acid E Glu
Glycine G Gly
Histidine H His

45. Amino Acids found in Proteins
Isoleucine I Ile
Leucine L Leu
Lysine K Lys
Methionine M Met
Phenylalanine F Phe
Proline P Pro
Serine S Ser
Threonine T Thr
Tryptophan W Trp
Tyrosine Y Tyr
Valine V Val

47. Sl
no.
Na
me
Structure
1. Glycine
2. Alanine
symbol
3 letters 1 letter
I. AMINO ACIDS WITH ALIPHATIC SIDE CHAIN
Gly G
Ala A
3. Valine Val V
-CH-COO-
NH+
3
-CH-COO-
NH+
3
CH3
-CH-COO-
NH+
3
H3C
CH
H3C

48. 4. Leucine Leu L
5. Isoleucine Ile I
II. AMINO ACID CONTAINING HYDROXYL (-OH) GROUP
6. Serine Ser S
7. Threonine Thr
T
-CH-COO-
NH+
3
-CH-COO-
NH+
3
H3C
CH-CH2
H3C
CH3
CH2
CH
H3C
-CH-COO-
NH+
3
-CH-COO-
NH+
3
20

49. III. SULFUR CONTAINING AMINO ACIDS
8. Cysteine Cys C
-CH-COO-
NH+
3
9. Methionine Met M
-CH-COO-
NH+
3
IV. ACIDIC AMIO ACIDS AND THEIR AMIDES
10. Aspartic acid Asp D
-CH-COO-
NH+
3
11. Asparagine Asn N
-CH-COO-
NH+
3

50. 12. Glutamic acid Glu E
-CH-COO-
NH+
3
13. Glutamine Gln Q
-CH-COO-
NH+
3
v. Basic amino acids
14. Lysine Lys K
-CH-COO-
NH+
3
15. Arginine Arg R NH-CH2-CH2-CH2
C=NH+
2
NH2
-CH-
COO-
NH+
3

51. 16. Histidine His H
-CH-COO-
NH+
3
VI. AROMATIC AMINO ACIDS
17. Phenylalanine Phe F
-CH-COO-
NH+
3
18. Tyrosine Tyr Y -CH-COO-
NH+
3
19. Tryptophan Trp W
-CH-COO-
NH+
3

52. VI. Imino acid
20. Proline Pro P
N COO-
H

53. Biochemical Importance of Amino Acids
Amino
Acids
Glycine
Systematic
name
Aminoetha-
noic acid
Alanine α-amino
propanoic
acid
Importance
Helps trigger the release of oxygen to
the energy requiring cell-making
process
Important in the manufacture of
hormones for strong immune system
ImportantAA as it is an energy source
for the liver, muscles, and CNS
Strengthens the immune system by
producing antibodies
Helps in the metabolism of sugars and
organic acids

54. Valine α-amino 3-
methylbutanoic
acid
Leucine α-amino
4-methyl
pentanoic acid
Isoleucine α-amino 3-
methylpentanoic
acid
Essential AA
Promotes mental vigor,
muscle coordination and
calm emotions
Essential AA
Provides necessary
substances for energy
production
Stimulants to the upper
brain and helps to be more
alert
Essential AA
Same functions as leucine

55. Phenylalanine α-amino 3-
phenylpropanoic
acid
Tyrosine α-amino 3-(4-
hydroxyphenyl)prop
anoic acid
Essential AA
Usedby the brain to produce
norepinephrine,
Reduces hunger pains
Functions as antidepressant
Helps improve memory
Transmits nerve impulses to the brain;
helps overcome depression; improves
memory; increases mental alertness;
promotes the healthy functioning of the
endocrine glands
Tryptophan α-amino 3-indole
propanoic acid
Essential AA
Anatural relaxant, helps alleviate insomia by
inducing normal sleep
Reduces anxiety and depression
Helps in the treatment of migraines and
headaches
Helps stabilize the immune system
Helps reduce risk of artery and heart spasms
Works with lysine in reducing cholesterol levels

56. Methionine α-amino 4-
methyl thiol
butanoic acid
Essential AA
Principal supplier of sulfur which
prevents disorder of the hair, skin
and nails
Helps lower cholesterol levels by
increasing the liver’s production of
lecithin
Anatural chelating agent for heavy
metals
Regulates the formation of
ammonia and creates ammonia-free
urine which reduces bladder
irritation
Influences hair follicles and
promotes hair growth

57. Cysteine 2-amino 3-
mercaptopropanoic
acid
Serine 2-amino 3 hydroxy
propanoic acid
Threonine 2-amino 3 hydroxy
butanoic acid
Functions as an antioxidant and is a
powerful aid to the body in protecting
against radiation and pollution
Helps slow down the aging process,
deactivate free radicals, neutralizes toxins
Aidsin protein synthesis and promotes
cellular repair
Necessary for skin formation, in the
recovery from burns and surgical operations
Astorage source of glucose by the liver
and muscles
Helps strengthen immune system by
providing antibodies
Synthesizes fatty acid sheath around nerve
fibers
Essential AA
Important constituent of collagen,
Assists metabolism and assimilation
Helps the digestive and intestinal tracts
functions normally
Helps prevents fat build-up in the liver

58. Histidine α-amino 3 (1H-
imidazol-4-yl)
propanoic acid
Lysine 2,6 diamino
hexanoic acid
Arginine α-amino 5-
guanidino
pentanoic acid
Essential AA
Found abundantly in hemoglobin
Usedin the treatment of rheumatoid
arthritis, allergic diseases, ulcers, anemia
Essential AA
Insures adequate absorption of calcium
Helps form collagen (which makes up
bone and cartilages)
Aidsin the production of antibodies,
hormones and enzymes
Helps improve immune responses to
bacteria, viruses and tumor cells
Promotes wound healing and
regeneration of the liver
Causes the release of growth hormones
Crucial for optimal muscle growth and
tissue repair

59. Aspartic Acid α-amino
butanedioic acid
Glutamic
acid
α-amino
pentanedioic acid
Asparagine α-amino 3
carbamoyl
propanoic acid
Mosteasily used as energy source
Aidsin the expulsion of toxic ammonia
from the body
Located most closely to the TCA cycle,
the site of energy production
Found in increased levels in people with
epilepsy and in decreased amounts in
some cases of depression
Considered to be nature’s “brain food” by
improving mental capacities
Helps speed the healing of ulcers; gives
a “lift” from fatigue
Helps control alcoholism, schizophrenia
and the craving of sugar, Parkinson’s
disease, mental retardation, and muscular
dystrophy
Found in the surfaces of proteins where
they can interact with water molecules

60. Glutamine α-amino 4
carbamoyl
butanoic acid
Found in the surfaces of proteins where
they can interact with water molecules
The polar amide groups can also form
hydrogen bonds with atoms in the side
chains of other polar amino acids
Proline Pyrrolidine-2-
carboxylic acid
Non-essential AA
Important for the proper functioning of
joints and tendons
Helps maintain and strengthen heart
muscles
Helps repair processes after cell injury or
for any type of wound healing
Hydroxy
lysine
Hydroxy
hexanoic acid
Itis a hydroxy derivative of lysine.
Itis most widely known as a component
of collagen