Amino Acids, Peptides and

Proteins

LUDITHA LUMAPAT-PE, MD, CFP, FPAAB

Chair, Department of Biochemistry
 The Proteins speak:
“We are the basis of structure
and function of life;
Composed of twenty amino acids,
the building blocks;
Organized into primary, secondary, tertiary
and quaternary structure;
Classified as simple, conjugated
and derived proteins.”
 AMINO ACIDS

-group of organic compounds

containing two functional
groups:

amino group (-NH2)  basic

carboxyl group (-COOH) acidic
 General Structure of Amino
Acids

H H

R C COOH R C COOH

NH2 NH3

General Structure Exists as ion

α - amino acids

amino
groups – attached to the
carboxyl same carbon Atom

α - carbon atom  binds to a side chain 

represented by R (different for
each of the 20 amino acids
found in proteins)

Ionized forms  how they exist

Classification of Amino Acids
based on polarity
of the R group

4 groups

Polarity  reflects the functional role

of AA in protein structure
1. Non-polar AA

hydrophobic (water hating)

No charge on the ‘R’ group
Examples are:
Alanine Methionine
Leucine Phenylalanine
Isoleucine Tryptophan
Valine Proline
2. Polar AA with no charge
on ‘R’ group

no charge on the ‘R’ group

possess groups  hydroxyl
sulfhydryl
amide
participate in hydrogen bonding of
protein structure
Examples:
Asparagine Glycine Cysteine
Tyrosine Serine Threonine
Glutamine
3. Polar AA with (+) ‘R’ group

carries (+) charge

Examples:
Histidine Arginine Lysine

4. Polar AA with (-) ‘R’ group

• carries (-) charge

• Examples:
Glutamic Acid Aspartic Acid
 PROPERTIES OF AA
- they differ in their
physicochemical properties
which ultimately determine
the characteristics of proteins
A.Physical Properties
1. Solubility - soluble in water and insoluble in
organic solvents

2. Melting Points - melt at higher temperatures

often 200°C

3. Taste
sweet (Gly, Ala, Val)
tasteless (Leu)
bitter (Arg, Ile)
Sodium Glutamate
– salt of Glutamic Acid – flavoring agent
4. Optical Properties
- Assymetric  a carbon atom is
attached to 4
different groups

exhibiting optical isomerism

4 distinct groups R
H
COOH
NH3
All AA except Glycine possess
optical isomers due to
asymmetric α-carbon atom

Some AA (Isoleucine, Threonine)

 2nd asymmetric carbon
 D- and L- forms of AA based on
the structure of glyceraldehyde

CHO CHO

H C OH OH C H

CH2OH CH2OH

D-Glyceraldehyde L-Glyceraldehyde
 R R

H C NH2 H2 N C H

COOH COOH

D-Amino Acid L-Amino Acid

The proteins are composed of L-α amino

acids
5. Amino acids as ampholytes

can donate a proton or accept a

proton

AA contain both acidic (-COOH)

and basic (-NH2) groups
 Zwitterion or dipolar ion:

Zwitter
 from German word – means
“hybrid”

Zwitter ion (or dipolar ion)

 a hybrid molecule containing (+) and
(-) ionic groups
AA rarely exist in a neutral form with free
carboxylic (-COOH) and free Amino (-NH2)
groups

Strongly acidic pH (low pH)  AA (+)

charged (cation)

Strongly alkaline pH (high pH)  AA (-)

charged (anion)

Each AA has a characteristic pH (e.g. Leucine,

pH – 6.0), at which it carries both (+) and (-)
charges and exist as zwitterion
 Existence of an amino acid as Cation, Anion and
Zwitterion
H

H໋ R C COOH H໋
NH2
H Amino Acid H

R C COOH R C COO ¯

NH3໋ NH2
Cation (low pH) Anion (high pH)
H H

N
R C COO_
NH
Zwitterion (Isoelectric pH)
 Isoelectric pH (symbol pI)

the pH at which a molecule exists as a

Zwitterion or dipolar ion and carries
no net charge

Molecule is electrically neutral

 Calculation of the pI value

take the average pka values corresponding to

the ionizable groups.

Example: Leucine has 2 ionizable groups

calculate pI as follows

pH= pk1 (COOH) + pk2 (NH3 )

+

pI = 2.3 + 9.7 = 6.0

2
Leucine

exists as cation at pH below 6 and

anion at pH above 6

at the isoelectric pH (pI = 6.0), Leucine

is found as Zwitterion
B. Chemical Properties
General Reactions  mostly due to the 2
functional groups

Reactions due to - COOH group

1. AA form salts (-COONa) with bases
and esters (-COOR’) with alcohols

2. Decarboxylation
- AA undergo decarboxylation to produce
corresponding amines
 R CH COO¯ R CH2 + CO2

NH3 + NH3 +

this reaction assumes significance in the living cells due to

the formation of many biologically important amines
include histamine from (Histidine)
tyramine from (Tyrosine)
α-Amino butyric Acid (GABA)
from (Glutamine)
3. Reaction with Ammonia

- the carboxyl group of dicarboxylic

AA reacts with NH3 to form amide

Asparatic Acid + NH3  Asparagine

Glutamic Acid + NH3  Glutamine
Reactions due to -NH2 group

4. The Amino groups behave as bases and

combine with acids (e.g. HCl) to form
salts (-NH3 + Cl¯)

5. 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 

Ruhemman’s purple

Ninhydrin reaction – quantitative

determination of AA and proteins
6. Colour reactions of Amino Acids
- AA can be identified by specific colour
reactions
Color Reactions of proteins / AA
Reaction Specific group or AA
1. Buiret Reaction Two peptide linkages
2. Ninhydrin Reaction α-Amino acids
3. Xanthoproteic Reaction Benzene ring of
aromatic AA (Phe, Tyr,
Trp)
4. Million’s reaction Phenolic Group (Tyr)
5. Hopkins – Cole Reaction Indole Ring (Trp)
6. Sakaguchi Reaction Guanidino Group
(Arg)
7. Nitroprusside Reaction Sulfhydryl groups
(Cys)
8. Paulys’ test Imidazole ring (His)
9. Sulfur test Sulfhydryl groups
(Cys)
10. Folin – Coicalteau’s Phenolic groups
test (Tyr)
7. Transamination
- important reaction in AA metabolism
- transfer of an amino group from an amino
acid to a keto acid to form a new AA

8. Oxidative deamination
- AA undergo oxidative deamination to
liberate free ammonia