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:

(-NH2) basic
carboxyl group (-COOH) acidic
amino group

General Structure of Amino Acids

H

COOH

NH2

General Structure

COOH

NH3

Exists as ion

 - amino acids

amino
groups

attached to the
same carbon Atom

carboxyl

- carbon atom

binds to a side chain

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

represented by R

Ionized forms

how they exist

Classification of Amino Acids

based on polarity
of the R group

4 groups

Polarity

reflects the functional

role
protein structure

of AA in

1.

Non-polar AA

hydrophobic (water hating)

No charge on the R group
Examples are:

Alanine

Methionine

Leucine

Phenylalanine

Isoleucine

Tryptophan

Valine

Proline

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

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

Tyrosine

Serine

Threonine

Glutamine

Cysteine

Properties of
Amino Acids
- 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

temperatures

- melt at higher
often 200C

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

an
COOH

carbon
NH3

- held by
-

All AA except Glycine possess

optical isomers due to
asymmetric -carbon atom
Some AA (Isoleucine, Threonine)
2nd asymmetric carbon

D- and L- forms of AA based on

the structure of glyceraldehyde
CHO

CHO

OH

OH

CH2OH

D-Glyceraldehyde
Glyceraldehyde

CH2OH

L-

NH2

H2N

COOH
D-Amino Acid

COOH
L-

Amino Acid

The proteins are composed of L- 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

COOH

NH2
H

Amino Acid

COOH

COO

NH3
Cation
(low pH)

NH2

H
R

pH)

NH

COO

Anion
(high

Isoelectric pH (symbol pI)

the pH at which a
molecule exists as
a Zwitterion or
dipolar ion and
carries
no net
charge
Molecule

is

Calculation of the pI value

take the average

pka values
corresponding to
the ionizable
groups.
Example: Leucine has
ionizable groups
calculate pI as
follows
pH =

pk1

(COOH)

pk2

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

B. Chemical Properties
General Reactions

mostly due to the 2

functional groups

Reactions due to - COOH group

1. AA from salts (-COONa) with bases

and esters (-COOR) with alcohols
2. Decarboxylation
- AA undergo decarboxylation to
produce
amines

corresponding

CH

COO
R

CH2 + CO2

NH3
NH3

this reaction
assumes
significance in the
living cells due to

3. Reaction with Ammonia

- the carboxyl group of dicarboxylic
AA reacts

with NH3 to form amide

Asparatic Acid + NH3

Glutamic Acid + NH3

Asparagine
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 -AMINO ACIDS react with
Ninhydrin to form a

purple, blue or

pink colour complex (Ruhemanns

purple)

Amino acid + Ninhydrin

Keto acid

+ NH3 + CO2

Hydrindantin

Hydrindantin + NH3 + Ninhydrin

Ruhemmans
purple

Ninhydrin reaction quantitative

determination of

AA

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.
2.
3.

Buiret Reaction
Ninhydrin Reaction
Xanthoproteic Reaction

4.
5.

Millions reaction
Hopkins Cole Reaction

Two peptide linkages

-Amino acids
Benzene ring of
aromatic AA (Phe, Tyr,
Trp)
Phenolic Group (Tyr)
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 Coicalteaus
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