Structure, properties and reactions of amino acids for undergraduate medical and biochemistry students

1. Chemistry of Amino Acids
R.C. Gupta
M.D. (Biochemistry)
Jaipur, India

2. Amino acids are the building blocks of
proteins
Living cells produce a vast array of proteins
Proteins are among the most important
biomolecules
Proteins perform a variety of biological
functions

3. Structure and function of
a protein depend upon the:
Nature of amino acids present in it
Sequence in which the amino
acids are present
Spatial relationship of amino acids
with one another

4. Carboxylic acids having one or more
amino groups
Carbon atoms are numbered 1, 2, 3 etc
starting from the carboxyl group
Also named a, b, g etc starting from
carbon atom next to the carboxyl group
Amino acids

5. R — CH2 — CH2 — CH2 — COOH
The amino group may be attached to any of
the carbon atoms next to the carboxyl group
The amino acid is accordingly known as a-
amino acid (2-amino acid), b-amino acid (3-
amino acid), g-amino acid (4-amino acid) etc
4 3 2 1
g b a

6. R — CH — CH — CH — COOH2 2
|
NH2
|
NH2
a-Amino acid (2-amino acid)
R — CH — CH — CH — COOH2 2
b-Amino acid (3-amino acid)
R CH CH CH COOH2 2— — — —
g-Amino acid (4-amino acid)
|
NH2

7. Proteins are made up of only a-amino
acids
The amino acid can exist as a D-isomer
and an L-isomer
Therefore, they exhibit stereo-isomerism
and optical isomerism
The a-amino acids contain at least one
asymmetric carbon atom

8. RR
|
R
|
H — C* —NH2
|
COOH
D-Amino acid L-Amino acid
H2N— C* — H
|
COOH
D- and L- Isomers
Amino group is present on right hand
side of a-carbon* in D-amino acids,
and on left hand side in L-amino
acids

9. Glycine is the only amino acid that has no
asymmetric carbon atom and, hence, no
stereoisomers
Threonine, isoleucine, hydroxylysine and
hydroxyproline have two asymmetric carbon
atoms, and hence four stereoisomers each

10. Proteins are made up of only L-isomers
of a-amino acids
Only 20 amino acids are used to
synthesize proteins
These are known as standard amino
acids

11. Classification
Amino acids can be
classified:
According to their polarity
According to the nature of their
side chains
On the basis of their nutritional
importance

12. The side chain of the amino acid may
be polar or non-polar
Accordingly, the amino acids may be
polar or non-polar amino acids
Classification according to polarity

13. Polar and non-polar amino acids
Non-polar amino
acids
• Have no ionizable
groups in side chain
• Include alanine,
valine, leucine,
isoleucine,
methionine,
phenylalanine,
tryptophan and
proline
Polar amino
acids
• Have ionizable
groups in side chain
• Include glycine,
serine, threonine,
cysteine, aspartate,
glutamate,
asparagine,
glutamine, tyrosine,
lysine, arginine and
histidine

14. They are less polar and less soluble in polar
solvents than the polar amino acids
However, non-polar amino acids are not
absolutely non-polar

15. In trans-membrane proteins:
The polar amino acids are
present outside or inside the
membrane
Non-polar amino acids are
generally embedded in the lipid
bilayer

16. Polar amino
acids
Non-polar amino acids

17. The side chains of amino acids may
differ in chemical nature
The amino acids may be divided into
several groups on this basis
Classification according to nature
of side chain

18. According to chemical nature of side
chains, amino acids can be divided
into those having:
• Aliphatic side chains
• Side chains having hydroxyl group
• Side chains containing sulphur
• Side chains having acidic groups or
their amides
• Side chains having basic groups
• Side chains containing aromatic rings
• Imino group

19. 1. Amino acids with aliphatic side chains
H — CH — COOH
|
NH2
CH — CH — COOH
|
NH
3
2
Glycine (Gly or G) Alanine (Ala or A)
CH—CH—COOH
NH2
CH3
CH3
Valine (Val or V)
CH — CH — COOH
|
NH2
CH2
CH3
Isoleucine (Ile or I)
CH3
CH —CH2— CH —COOH
|
NH2
CH3
CH3
Leucine (Leu or L)
|

20. CH — CH — COOH
|
OH
2
|
NH2
Serine (Ser or S)
CH — CH — CH — COOH3
|
OH
|
NH2
Threonine (Thr or T)
2. Amino acids with side chains having hydroxyl
group

21. CH — CH — COOH2
|
SH
|
NH2
Cysteine (Cys or C)
CH — S — CH — CH — CH — COOH3 2 2
|
NH2
Methionine (Met or M)
3. Amino acids with side chains containing sulphur

22. 4. Amino acids with side chains having acidic groups
or their amides
CH2 CH COOH
COOH NH2
Aspartate (Asp or D)
CH2 CH COOH
CONH2NH2
Asparagine (Asn or N)
CH2 CH2 CH COOH
COOH NH2
Glutamate (Glu or E)
CH2 CH2 CH COOH
CONH2 NH2
Glutamine (Gln or Q)

23. 5. Amino acids with side chains having basic groups
HN — CH — CH — COOH2 CH — CH —2 2
|
C= NH
|
NH2
|
NH2
Arginine (Arg or R)
CH — CH — COOH2 CH — CH — CH —2 2 2
|
NH2
|
NH2
Lysine (Lys or K)
— CH — CH — COOH2
|
NH2
Histidine (His or H)
NHN

24. 6. Amino acids with side chains containing aromatic
rings
—CH2—CH—COOH
|
NH2
Tyrosine (Tyr or Y)
HO‒
—CH2—CH—COOH
|
NH2
Tryptophan (Trp or W)
N
H
—CH2—CH—COOH
|
Phenylalanine (Phe or F)
NH2

25. 7. Imino acids
COOH
Proline (Pro or P)
N
H

26. Lysine and proline can be hydroxylated
after their incorporation into proteins
N
H
COOH
HO
CH2— CH — CH2— CH2— CH — COOH
|
NH2
|
NH2
|
OH
Hydroxylysine (Hyl) Hydroxyproline (Hyp)
They are converted into hydroxylysine
and hydroxyproline respectively

27. Two cysteine residues in a protein may be
linked through their –SH groups to form a
cystine residue
CH2— CH — COOH
|
S
|
NH2
CH2— CH — COOH
|
NH2
|
|
S
Cystine

28. Some enzymes contain an unusual
amino acid, selenocysteine, at their
catalytic site
Selenocysteine
SeH
CH2— CH — COOH
| |
NH2

29. Selenocysteine
Formed by replacing oxygen atom in
the side chain of serine by Se
The replacement occurs before
incorporation of serine in the protein
Glutathione peroxidase is an
example of a selenocysteine-
containing enzyme

30. Classification according to
nutritional importance
According to nutritional importance,
amino acids may be divided into:
Essential
amino
acids
Semi-
essential
amino
acids
Non-
essential
amino
acids

31. Proteins are synthesized from 20 standard
amino acids
However, some of these amino acids can
be synthesized in our body
Essential amino acids
All the standard amino acids are equally
important for protein synthesis

32. Some of the standard amino acids cannot
be synthesized by human beings
These amino acids are known as essential
amino acids
If these are not provided in diet, protein
synthesis will be impaired

33. Thus, the essential amino acids are
nutritionally indispensable
Valine, leucine, isoleucine, threonine,
methionine, lysine, phenylalanine and
tryptophan are essential amino acids
Animal proteins generally contain all the
the essential amino acids

34. Synthesis of semi-essential amino acids is
below their requirement in childhood
Hence, they must be provided in the diet
of children
Arginine and histidine are semi-essential
amino acids
Semi-essential amino acids

35. Endogenous synthesis of non-essential
amino acids can meet our requirement
Hence, their presence in the diet is not
essential
Glycine, alanine, serine, cysteine, aspartate,
glutamate, asparagine, glutamine, tyrosine
and proline are non-essential amino acids
Non-essential amino acids

36. Besides the 20 standard amino acids, some
other L-a-amino acids are also found in
human beings
These are either intermediates or products
of various metabolic pathways
Non-standard amino acids

37. The non-standard L-a-amino acids are:
• Homoserine
• Homocysteine
• Dihydroxyphenylalanine (DOPA)
• Mono-iodo-tyrosine (MIT)
• Di-iodo-tyrosine (DIT)
• Tri-iodo-thyronine (T3)
• Tetra-iodo-thyronine (T4)
• Ornithine
• Citrulline
• Argininosuccinic acid

38. CH — CH — COOH2 CH —2
|
OH
|
NH2
Homoserine
CH — CH — COOH2 CH —2
|
SH
|
NH2
Homocysteine

39. ‒CH2‒CH‒COOH
NH2
I
HO
Dihydroxyphenylalanine (DOPA)
HO‒
‒CH2‒CH‒COOH
NH2
I
I
Mono-iodo-tyrosine (MIT)
HO‒
‒CH2‒CH‒COOH
NH2
I
I
I
Di-iodo-tyrosine (DIT)
HO‒

40. ‒O‒ ‒CH2‒CH‒COOH
NH2
I
I
I
I
I
Tetra-iodo-thyronine (T4)
HO‒
‒O‒ ‒CH2‒CH‒COOH
NH2
I
I
II
Tri-iodo-thyronine (T3)
HO‒

41. Ornithine
CH — CH — CH — CH — COOH2 2 2
|
NH2
|
NH2
CH — CH — CH — CH — COOH2 2 2
|
NH
|
C — NH — CH
COOH
|
|
CH
|
COOH
2
||
NH
|
NH2
Argininosuccinic acid
Citrulline
CH — CH — CH — CH — COOH2 2 2
|
NH
|
C = O
|
NH2
|
NH2

42. CH2— CH2— COOH
|
NH2
b-Alanine
CH2— CH— COOH
|
NH2
|
CH3
b-Aminoisobutyric acid
CH2—CH2—CH2—COOH
|
NH2
g-Aminobutyric acid
CH2— CH2— SO3H
|
NH2
Taurine
Some non-a-amino acids are also present
in human beings
Examples are b-alanine, taurine, b-amino-
isobutyric acid, g-aminobutyric acid etc

43. b-Alanine is a constituent of pantothenic
acid, acyl carrier protein and coenzyme A
g-Aminobutyric acid (GABA) is a neuro-
transmitter
b-Aminoisobutyric acid is a metabolite of
some pyrimidines
Taurine is a neurotransmitter, and is a
constituent of bile acids and bile salts

44. Physical properties
Amino acids are crystalline solids
All amino acids have high melting
points
Aromatic amino acids absorb
ultraviolet light
They are soluble in polar solvents

45. Chemical properties
• Amphoteric nature
• Formation of peptide bonds
• Reactions of carboxyl and amino
groups
• Reactions of sulphydryl groups
• Reactions used for protein sequencing
• Reactions for identification of specific
amino acids

46. All amino acids have at least one
carboxyl and one amino group
Amphoteric nature
Both these groups are ionizable
R‒COOH R‒COO‒ + H+
R‒NH2 + H+ R‒NH3
+

47. R–COOH and R–NH3
+ are acidic forms as
they can donate hydrogen ions (protons)
Thus, amino acids can act as acids (proton
donors) as well as bases (proton acceptors)
R–COO– and R–NH2 are conjugate bases
as they can accept hydrogen ions

48. Therefore, amino acids are said to be
amphoteric in nature
They can behave as acids as well as
bases depending upon the pH of the
medium in which they are present

49. The amino acid, therefore, behaves as an
acid in an alkaline medium
In an alkaline medium, the carboxyl
group is dissociated while ionization of
amino group is suppressed
R‒CH‒COOH R‒CH‒COO‒ + H+
I I
NH2
NH2

50. Thus, the amino acid acts as a proton
acceptor (base) in an acidic medium
In an acidic medium, the amino group is
ionized while ionization of carboxyl group
is suppressed
NH3
+
R‒CH‒COOH + H+ R‒CH‒COOH
I I
NH2

51. There is a certain pH at which both
carboxyl and amino groups are ionized
NH3
+
R – CH – COO‾
This form of amino acid is known as a
zwitterion
The carboxyl group is un-protonated
and the amino group is protonated

52. Both carboxyl and amino groups are
ionized in a zwitterion, yet it is electrically
neutral as a whole
It does not move in an electric field
The pH at which an amino acid exists in
the zwitterion form is known as its
isoelectric pH or isoelectric point (i.e.p.)

53. Isoelectric pH is constant for every amino
acid
Solubility of the amino acid is the least at
its isoelectric pH
Completely un-dissociated form of amino
acids is shown frequently for the sake of
simplicity
It does not exist in solution at any pH

54. Strength of an acid depends on the degree
to which it dissociates and liberates protons
Strength of acids is generally expressed in
terms of their dissociation constants
Since amino acids are very weak acids,
their strength is expressed in terms of pK

55. pK is the negative log of dissociation
constant
The pK of the a-carboxyl groups of amino
acids is around 2.1
The pK of the a-amino groups is around
9.8
This means that R–NH3
+ form is weaker
than the R–COOH form as acid

56. One of the most important reactions of
amino acids
The bond by which amino acids are linked
with each other in peptides and proteins
Formed between carboxyl group of one
amino acid and amino group of another
amino acid
Formation of peptide bonds

57. H2N‒CH‒C‒N‒CH‒COOH
R1 R2O H
H2O
Amino acid 1 Amino acid 2
Dipeptide
Peptide bond
►
►
R1
H2N‒CH‒COOH
R2
H2N‒CH‒COOH

58. Formation of peptide bonds in living
cells is a complex process
The reaction occurs in stages, and
requires the presence of enzymes,
coenzymes and other factors

59. The peptide has a free ‒NH2 group at one
end and a free ‒COOH group at the other
The former is known as the amino end
and the latter as the carboxyl end
↑
Amino end
↑
Carboxyl end
-COOHH2N- AA AA AA AA AA AA AA AA

60. Amino end is also known as N-terminus
and the carboxyl end as C-terminus
All peptides and proteins possess an N-
terminus and a C-terminus
↑
N-Terminus
↑
C-Terminus
-COOHH2N- AA AA AA AA AA AA AA AA

61. Reactions of carboxyl and amino groups
The carboxyl and amino groups
of amino acids can undergo their
usual reactions such as:
Acylation Esterification
Formation
of salts

62. The sulphydryl (‒SH) group of cysteine can
undergo reversible oxidation and reduction
Disulphide bonds can be formed between the
‒SH groups of two cysteine residues
The ‒SH groups are essential for the
biological activity of many proteins
Reactions of sulphydryl groups

63. ‒ N ‒ CH ‒ C ‒
|
S
|
|
H
|
|
S
Cysteine
residue
CH2
CH2
|
‒ N ‒ CH ‒ C ‒
|
H
||
||
O
O
Cysteine
residue
Disulphide bond

64. Determination of amino acid sequence is
important for elucidating the structures of
proteins
Generally, the N-terminal amino acid is
tagged with some reagent
Reactions for determining amino acid
sequence of proteins

65. The tagged amino acid is split off by
hydrolysis, and is identified
The reaction is, then, repeated with the
new N-terminal amino acid and so on
Complete sequence of amino acids can,
thus, be determined

66. Common reactions used for
determining amino acid
sequence are:
Sanger’s
reaction
Edman’s
reaction

67. The amino group of the N-terminal amino
acid residue is tagged with 1-fluoro-2,4-
dinitrobenzene (Sanger’s reagent)
The tagged amino acid is split off and
identified
Sanger’s reaction

68. HF
1-Fluro-2,4-dinitrobenzene
N-Terminal amino acid residue
N-Terminal amino acid residue
tagged with 2,4-dinitrobenzene
O2N—
NO2
— HN—CH—C—
R O
O2N—
NO2
—F
H2N—CH—C—
R O



69. Amino group of N-terminal amino acid
residue is tagged with phenylisothiocynate
to form phenylthiohydantoic acid
The latter is converted into phenylthio-
hydantoin in the presence of an acid and
nitromethane
Edman’s reaction

70. S
||
—NH—C—NH—CH—C—
R
|
O
||
Phenylisothiocyanate
N-Terminal amino
acid residue Phenylthiohydantoic acid residue
H2O
Acid,
nitromethane
Phenylthiohydantoin Phenylthiohydantoic acid
S
||
C
CH
|
R
C
||
O
—NH NH
OH
S
||
C
CH
|
R
C
||
O
—N NH

—N=C=S
H2N—CH—C—
R O
►

71. These reactions are used for qualitative
detection and/or quantitative measure-
ment of amino acids
These reactions are given by free amino
acids as well as amino acids present in
peptides and proteins
Reactions for identification of specific
amino acids

72. Some important reactions of amino
acids are:
• Ninhydrin reaction
• Xanthoproteic reaction
• Millon-Nasse reaction
• Aldehyde reaction
• Hopkins-Cole reaction
• Sakaguchi’s reaction
• Lead sulphide reaction

73. This reaction is given by all amino acids
and peptides
The a-amino acids react with two
molecules of ninhydrin
A blue-purple coloured complex is formed
(proline gives a yellow colour)
The reaction occurs in stages
Ninhydrin reaction

74. O‒NH4
+
|
||
O
—N=
O
||
||
O
Coloured complex
O
||
||
O
OH
OH
Ninhydrin
a-Amino acid
R—CH—COOH
|
NH2
R—CHO + CO2 + NH3
O
||
||
O
OH
H
Reduced ninhydrin
O
||
||
O
OH
OH
Ninhydrin
2 NH3

75. This reaction is given by aromatic amino acids
(phenylalanine, tyrosine and tryptophan)
On boiling with concentrated HNO3, the phenyl
groups are converted into nitrophenyl groups
These ionize on addition of an alkali, and
impart an orange colour to the solution
Xanthoproteic reaction

76. This reaction is given by the 3,5-unsubs-
tituted hydroxyphenyl group of tyrosine
Mercuric sulphate and nitrous acid cause
mercuration and nitration or nitrosation of
the hydroxyphenyl group of tyrosine
This produces a red colour
Millon-Nasse reaction

77. This reaction is given by the indole ring of
tryptophan
The indole ring reacts with formaldehyde,
in the presence of sulphuric acid, to form a
violet complex
Aldehyde reaction

78. This is similar to the Millon-Nasse reaction
The aldehyde here is glyoxylic acid
(HOOC–CHO)
This reacts with the indole ring of
tryptophan in the presence of sulphuric
acid to form a violet complex
Hopkins-Cole reaction

79. This reaction is given by the guanidino group
of arginine
In a basic medium, a-naphthol reacts with the
guanidino group forming a complex
On adding sodium hypobromite/hypochlorite,
the complex is oxidized to a red coloured
product
Sakaguchi’s reaction

80. This reaction is given by sulphur-containing
amino acids, cysteine and cystine
On boiling with sodium hydroxide, the
sulphur present in these amino acids is
released in the form of sodium sulphide
This reacts with lead acetate to form a
brown or black precipitate of lead sulphide
Lead sulphide reaction

81. Methionine contains sulphur but it does not
give lead sulphide reaction
Sulphur present in methionine is not
released on boiling with sodium hydroxide