1. Chemistry of Amino acids
Dr. V.P.Acharya
Professor Biochemistry
IMS & SUM Hospital
2. Learning objectives
• Why study proteins?
• What do they do for us?
• What are they made of?
• Amino acids
• Classification of Amino acids
• Properties of AA
• Classification of proteins
• Properties of proteins
• Determination of protein structure
• Structural organisation of proteins
• Plasma proteins
• Immunoglobulins
3. Proteins- Proteios (Greek)
• Proteios = Primary or holding first
place
• The word protein that I propose to
you . . . I would wish to derive from
proteios, because it appears to be
the primitive or principal substance
of animal nutrition that plants
prepare for the herbivores, and
which the latter then furnish to the
carnivores.
• —J. J. Berzelius, letter to G. J.
Mulder, 1838
6. Why study proteins?
• Proteins are very important biological molecules that play crucial
roles in virtually all biological processes
• 3/4th of total dry body weight- proteins
• Catalytic function:
Nearly all chemical reactions in biological systems are catalyzed by specific
enzymes.
• Transport and storage:
For example;
Hemoglobin transports oxygen in erythrocytes
Myoglobin carries & stores oxygen in muscle.
Albumin transports free fatty acids in blood.
Transferrin transports iron in blood.
• Coordinated motion: Actin and myosin are contractile proteins in muscle.
7. • Structural and Mechanical support:
e.g. collagen, a fibrous protein in skin and bone.
• Defense function:
e.g. Clotting factors prevent loss of blood.
Immunoglobulins protects against infections.
• Generation and transmission of nerve impulses:
e.g. Rhodopsin is the photoreceptor protein in retinal
rod cells.
• Control of growth and differentiation:
e.g. growth factor proteins.
hormones such as insulin and thyroid-stimulating
hormone.
• Genetic regulation:
9. Amino acids
• Building blocks of proteins
• Held by peptide bonds
• 300 amino acids in nature
• 20 AA make all the proteins (or is it 22?)-
human body
• All except Proline- α AA
• All AA have L-configuration (Exception: D-
serine & D-aspartic acid in brain)
• Genetic code specifies for 20 L-α- AA
10. All AA share a common structure
Amino group
Carboxyl
group
R varies in different AA
11. Naming of ‘C’ atoms
AA have a 3 letter abbreviation and 1 letter symbol
13. A. Based on structure
I. Aliphatic AA (Gly, Ala, Val, Leu, Ile)
II. Hydroxy amino acids (Thr, Ser, Tyr)
III. Sulphur containing AA (Cys, Met)
IV. Dicarboxylic acid and their amides (Glu, Gln,
Asp, Asn)
V. Di amino acids/ Basic AA (Lys, Arg, His)
VI. Aromatic AA (Phe, Tyr, Trp)
VII. Imino acid/ heterocyclic AA (Pro)
30. D. Classification based on metabolism
1. Purely ketogenic- Leu
2. Ketogenic and glucogenic- Lys, Ile, Phe, Tyr &
Trp
3. Purely glucogenic- rest 14 AA
31. 21st century witnesses addition of 21st
AA
SELENOCYSTEINE
incorporated as such into proteins during
protein synthesis
Has separate codon- a stop codon (UGA)
Selenium present
Some enzymes e.g. Thioredoxin reductase
SeCys or SeC (U)
32. Now 22nd AA discovered
Oops!
Another AA
to memorize
!!!
33. Pyrrolysine- 22nd AA
• Pyl
• Methyl transferase enzyme of bacteria
• Coded by one of the stop codons
34. Derived AA
• After protein biosynthesis some AA are
modified- Hydroxyproline, hydroxylysine
• Some remain free- Citrulline, Ornithine,
Homocysteine
• Non-alpha AA- Gamma amino butyric acid
from Glu; β- alanine
35. Special groups of AA
Arg – Guanidium gr
Phe – Benzene ring
Tyr- phenol
Trp – indole
His- imidazolium
Pro- pyrrolidine
38. • All AA are soluble in water and alcohol
• Insoluble in non- polar solvents
• Gly, Ala, Val, Ser, Trp, His, Pro- sweet
• Leu- tasteless
• Ile, Arg- bitter
• High melting points > 2000c
• Colorless
• Crystalline
• MW- 77-205D
Physical properties
40. All natural AA are L-α- Amino acid
• Non- superimposible mirror
images- - Enantiomers (a
class of stereoisomers)
• D= Dextro; L= Laevo
• D- AA- some microbes,
certain antibiotics,
Gramicidin S, Polymyxin,
Antimycin
• Ile, Thr- 2 optically inactive
centres
41. Ampholytes and Iso -electric point
Due to ionizing property of AA, they
exert:
Amphoteric properties (zwitterion)
Acid base behaviour
Buffering activity
42. • AA can exist as ampholytes/ zwitterions
depending on the pH of the medium
• Ampho= both
• COO- anion
• NH3
+ - cation
• Acidic pH- ↑H+ -- overall charge becomes +ve
• Basic pH- ↓H+ -- overall charge on molecule
becomes negative
C
O
OH
R
NH3
C
O
O
R
NH3
C
O
O
R
NH2
LOW pH
Zwitterion
NEUTRAL
Carboxylate Form
HIGH pH
ammonium Form
43. Isoelectric pH (pI)
• pH at which there’s no net charge on the molecule
i.e. they cancel each other’s charge
• No mobility in the electrical field
• Solubility is minimum- precipitate
• Buffering capacity is minimum
• Each AA has a unique pI
• Helpful in separating AA in a mixture
• pI for Gly = 6.0
Asp = 3.0
Lys = 9.8
Arg = 10.8
44. pK???
• From pI point if acid (HCl) is added drop by drop, at
a point 50% cation + 50% zwitterion– pK1
• From pI if NaOH is added drop by drop, at one point
50% anion + 50% zwitterion– pK2
• pH = pK1 + pK2/ 2
• Gly pI = 2.34 + 9.6 / 2= 5.97
• > 2 ionizable groups- more pKs
45. • His- pK value of
imidazolium gr-
6.1
• Hence most
effective buffer
• Plasma proteins &
Hb have maxm
buffering capacity
due to His
46.
47.
48. General reactions of AA
A. Due to carboxyl gr
B. Due to amino gr
C. Due to side chains
49. Reactions due to carboxyl gr
1. Decarboxylation: alpha decarboxylation to
form corresponding amines
Histidine→ Histamine + CO2
Tyrosine → Tyramine + CO2
Tryptophan →Tryptamine + CO2
Lysine → Cadaverine + CO2
Glutamic acid → gamma amino butyric acid
(GABA) + CO2
50. 2. Amide formation: The extra COOH gr of
dicarboxylic acid can combine with NH3-
amide
Aspartic acid + NH3 → Asparagine
Glutamic acid + NH3 → Glutamine
51. Reactions due to Amino gr
3. Transamination: α amino gr is transferred to α keto
acid to form the form a new AA and α keto acid.
52. 4. Oxidative deamination: α amino gr removed
↓
Corresponding keto acid + ammonia
Glu- most common to undergo oxidative
deamination
53. 5. Formation of carbamino compounds: CO2
adds to the α Amino gr → Carbamino gr
• Helps in transport of oxygen
• Alkaline pH
54. Reactions due to side chains
6. Transmethylation: Methyl gr of Met gets
transferred after activation
Met + acceptor
↓
Methylated acceptor + Homocysteine
55. 7. Ester formation by the OH gr:
Hydroxy AA (Ser, Thr) form
phosphoproteins with phosphoric acid
With carbohydrates- glycoproteins
56. 8. Reactions of the amide gr:
Gln & Asn- form N-glycosidic bonds in
glycoproteins
9. Reactions of -SH gr:
2 Cys -- Cystine
57. Peptide bond formation
• 2 AA join covalently by substituted amide
linkage releasing a molecule of H2O
• CO-NH
• Covalent linkage
58. Colour reactions of AA
Reaction Answered by specific
group
Ninhydrin α amino group
Biuret Peptide bonds
Xanthoproteic Aromatic AA
Millon’s test Phenol (Tyr)
Aldehyde test Indole (Trp)
Sakaguchi’s test Guanidium (Arg)
Sulphur test Sulfhydryl (Cys)
Nitroprusside test Sulfhydryl (Cys)