This document provides an overview of protein chemistry and amino acids. It defines amino acids as organic compounds containing amino and carboxyl groups. Amino acids combine via peptide bonds to form proteins. There are 20 standard amino acids that make up human proteins. Amino acids are classified based on structure, side chains, and metabolic fate. They have various physical and chemical properties important for protein structure and function. Amino acid derivatives also have biological significance as neurotransmitters, hormones, and drugs.

1. PROTEIN CHEMISTRY - I
By Dr ANURAG YADAV
Moderator Dr ARUN KUMAR K

2. Content :
 Definition of amino acids
 Definition of peptide bond
 General structure of amino acids
 Numbering of amino acids
 Nomenclature of amino acids.
 Classification of amino acids.
 Properties of amino acids.
 Biological importance of amino acid derivatives.

3. OVERVIEW:
 Proteins are most abundant & functionally diverse
molecule in living system.
Virtually every life process depends on this
class of molecules.
 Enzymes & polypeptide hormones direct & regulate
body metabolism.
 In bone, protein collagen forms a frame work for
deposition of salts.
 Immunoglobulin's fight against infectious bacteria &
viruses

4. DEFINITION
 Amino acids are group of organic compounds
containing two functional groups – amino and
carboxyl.

5. PEPTIDE BOND
 Is chemical bond formed between the α-carboxyl
groups and α-amino group of next amino acid.
 It’s the primary linkage of all protein structures.

6. NON STANDARD AMINO ACIDS:
 Amino acids can b classed as standard amino acids and
non standard amino acids.
 Of 300 amino acids human body codes 20 amino acids.
 These although never incorporated into structure of protein
, but play several biological role.
 These include :
D-amino acids: bact cell wall, antibiotics
Non-protein amino acids: taurine,homocysteine.etc.,
Amino acid derivatives: GABA, DOPA, hydroxy proline &
hydroxy lysine.

7. AMINO ACIDS
 They are monomer unit of proteins
 All major structural and functional aspect of body
are carried out by the proteins
 20 amino acids are seen in humans.
 Most of amino acids are in α-amino acids except
proline
General structure

8. NUMBERING OF AMINO ACID:

9. ABBREVIATIONS & SYMBOLS FOR AMINO
ACIDS
a) Unique letters first: if only one amino
acid begins with particular letter ,
than letter is used as
symbol.(I=Isoleucine).
b) Most commonly occurring Amino
Acid have priority if more than one
amino acid begin with particular
letter & it receive that letter as
symbol (Glycine>Glutamate; so
G=Glycine.

10. c) Similar sounding names :
F-Phenylalanine.
W-tryptophan.
d) Letter close to initial letter: is
assigned as symbol which is close to
first letter as close .
Eg: k- lysine

11. CLASSIFICATION OF AMINO ACIDS:
Based on structure
Based on side chain
Based on metabolic fate
Based on nutritional requirement

12. BASED ON STRUCTURE:
Aliphatic amino acids.
Aromatic amino acids.
Heterocyclic amino acids.
Imino acids.
Derived amino acids.

13. ALIPHATIC AMINO ACIDS:
Monoamino
monocarboxylic acids
Monoamino dicarboxylic
acids
Dibasic monocarboxylic
acids

14.  Simple amino acid: Glycine.
Alanine.
 Branched chain amino acids: Valine.
Leucine.
Isoleucine.

15.  Hydroxyamino acids: Serine.
Threonine.
 Sulfur containing amino acids: Cysteine.
methionine.

16.  Amino acid with Amide group: Glutamine.
Asparagine.
 Monoamino dicarboxylic acids: Aspartic acid.
Glutamic acid.

17.  Dibasic monocarboxylic acids: Lysine.
Arginine.
AROMATIC AMINO ACIDS:
Phenylalanine, Tyrosine.

18. HETEROCYCLIC AMINO ACIDS:
Tryptophan
Histidine
IMINO ACID: Proline.
Tryptophan(Trp)(W) with
indole group

19. Derived amino acids :
• Derived amino acid found in proteins:
Hydroxyproline
• Derived amino acid not found in proteins:
Ornithine and citrulline.
• Non alpha amino acids: GABA, βalanine.

20. SPECIAL GROUPS IN AMINO ACIDS:
Arginine Guanidinium group
Phenylalanine Benzene group
Tyrosine Phenol group
Tryptophan Indole group
Histidine Imidazole group
Proline Pyrrolidine group

21. BASED ON SIDE CHAIN:

22. Amino acids having Non-polar side chain:
 Has an Non-polar side chain that doesnot
gain/lose proton/particiate in hydrogen/ionic
bond.
 They are usually hydrophobic.
LOCATION:
 The side chain tends to cluster together in
interior of protein & this phenomenon is
called as hydrophobic effect.
 Eg: Alanine, Valine, Leucine, Isoleucine,
Proline, Phenylalanine, Tryptophan.

23. Amino acids with uncharged/Non-ionic polar:
 These are with ZERO net charge at neutral pH .
 These amino acids are hydrophilic.
 eg: Glycine, Serine, Threonine & Asparagine.

24. Amino acids having charged/Ionic polar side
chain:
a)Acidic amino acid: they are negatively charge on R
group. Eg: Aspartic acid.
Glutamic acid.
b) Basic amino acids: they have positive charge on R
group. Eg: Lysine.
Argenine.
Histidine.

25. BASED ON METABOLIC FATE:
a) Purely ketogenic: converted to ketone bodies (fat
can be synthesized from these amino acids).
Eg:Leucine
b) Both ketogenic & glucogenic: Lysine, isoleucine,
Phenylalanine, Tyrosine, Tryptophan are partially
ketogenic & glucogenic.
c) Purely glucogenic: all remaining 14 amino acids
are glucogenic as they enter only into the
glucogenic pathway.

26. BASED ON NUTRITIONAL REQUIREMENT:
Essential/indispensable
 Cannot be synthesized by
the body.
 Needed to be supplied in
diet.
 Phenylalanine, Valine,
Threonine, Trptophan,
lsoleucine, Methionine,
Leusine, Lysine
 Non-essential
 they can be synthesized by
body & need not to be
supplemented.
 Alanine, Aspargine,
Aspartate, Glutamate,
Glutamine, Tyrosine,
Serine, Proline, Glycine,
Cysteine.

27.  Semi-essential amino acids: they are synthesized by the
adults , but the growing children need to be supplemented
in food . They are
:Arginine
Histidine.
 Conditional essential amino acids: when person suffers
from chronic illness he lose ability to manufacture enough
Non-essential amino acids & hence need to be
supplemented.
- Arginine, Glycine, Cysteine, Tyrosine, Proline,
Glutamine & Taurine.

28. SELENOCYSTEINE- 21ST AMINO ACID
 21st amino acid
 Derivative of serine
 Structure similar to cysteine, but
with an atom of selenium(SeH)
taking place of sulphadryl (SH).
 Stop codon: UGA
 It’s present in active site of
several enzymes like
glutathione peroxidase.

29. PYRROLYSINE:
 22nd amino acid.
• lysine derivative encoded
by UAG codon
• Used by some
prokaryotes.
• Present in methyl
transferase enzyme of
bacteria.

30. PROPERTIES OF AMINO ACIDS:
Physical properties :
 They are colourless.
 Taste varies( glycine-sweet, leucine-tasteless,
arginine-bitter).
 Soluble in water .
 Melting point is higher >200°c.
 Optical activity.
 Ampholyte & Isoelectric point.

31. OPTICAL ACTIVITY:
 All amino acids have
asymmetric carbon atom
hence show optical isomers.
 Except glycine.
 The mirror image are
produced with reference to α-
carbon atom as D & L
isomers.

32. D & L ISOMERS
 L amino acid occur in nature & therefore called as
Natural amino acid
 D-amino acids are found in antibiotics & bacterial
cell wall.

33. AMPHOTERIC NATURE & ISOELECTRIC POINT
 At physiological pH amino acids exists as ions.
 They act as ampholyte/ zwitter ion in solution
depending on pH of the medium.
 In acidic medium acts as cations & in alkaline medium
as anion.

34.  All groups are ionized but
cancel eachother
 At this particular pH the
molecule carry no net charge
is known as Isolectric point &
these are called zwitter ions.
 hence there will be no
mobility in an electrical field.
 Solubility & buffering capacity
will be minimum.

35. TITRATION CURVE FOR AMINO ACID
pI= pK1 + pK2
2

36.  In case of amino acid having more than two
ionizable groups, correspondingly there will be
more pK values , eg: aspartic acid

37. Features of a molecule at iso-electric point:
 molecule minimally soluble & maximally
precipitated.
 Viscosity of substance is minimum.
 Buffering capacity is at its minimum.
 The conductivity & osmotic pressure are at
minimum.
 Molecule is electrically neutral.

38. CHEMICAL REACTIONS
Due to carboxyl group:
1. amino acids form salts (COONa) with bases &
ester (-COOR’ ) with alcohol.
2. Decarboxylation: form corresponding amine.
1. Histidine histamine + CO2
2. Tyrosine tyramine + CO2
3. Tryptophan tryptamine + CO2
4. Lysine cadaverine + CO2
5. Glutamic acid GABA + CO2

39.  Reactions with ammonia: the carboxyl group of
dicarboxylic AA other than α-carboxyl combine with
ammonia to form corresponding amide.
Aspartic acid
+NH3 = Asparagine. glutamic acid
+NH3= Glutamine.

40. REACTIONS DUE TO AMINO GROUP:
Transamination : α-amino
group transferred to α-keto
acid to form new amino
acid & α-keto acid.
Oxidative deamination:
removal of α-amino group
to form α-keto acids and
ammonia.

41. Formation of carbamino compound: in alkaline pH
CO2 adds to α-amino group to form carbamino
compound. It serves transport of CO2 by
hemoglobin.
Hb-NH2 Hb-NH-COOH

42. REACTIONS DUE TO SIDE CHAIN:
Transmethylation: the methyl group is transferrred;
Eg: methionine + acceptor methylated acceptor
+ homocysteine.
Ester formation by OH group:
Serine(OH)+Phosphoric acid Phosphoproteins
and also forms glycoproteins.

43. Reactions of amide group: glycoprotein is formed
when amide group of Glutamine & Asparagine
forms N-glycosidic bonds with carbohydrate.
Reaction of SH group: cysteine has a sulfhydryl
group it can form disulfide bond with another
residue. Can also connect two polypeptide chains
forming interchain disulfide bonds.

44. COLOR REACTIONS OF AMINO ACIDS &
PROTEINS
1.Ninhydrin Alpha amino group
2.Biuret reaction Peptide bonds
3.Xanthoproteic test Benzene ring(Phe,Tyr,Trp)
4.Millon’s test Phenol(Tyrosine)
5.Aldehyde test Indole(Tryptophan)
6.Sakaguchi’s test Guanidinium(Arginine)
7.Sulfur test Sulfhydryl(Cysteine)
8.Nitroprusside test Sulfhydryl(Cysteine)
9.Pauly’s test Imidazole(Histidine)

45. AMINO ACID DERIVATIVES OF IMPORTANCE
GABA:
 Derivative of glutamic acid & dopamine.
 A neurotransmitter
 GABA pentin can pass BBB & form GABA in brain.
Hitamine:
 Synthesized from histidine.
 Mediator in allergic reactions.

46. Thyroxine:
 From tyrosine.
 An thyroid hormone.
Cycloserine:
 Derivative of serine
 As an antituberculous drug
Histidine:
 Important in buffering.
Ornithine:
 & citrulline are derivative of arginine, essential for urea
synthesis.

47. REFERENCES:
 Text book of biochemistry- DM Vasudevan.
 Lippincott’s illustrated biochemistry.
 Biochemistry – U Satyanarayana.