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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.”
AM INO ACI DS

-group of org ani c


co mpo und s co nta ini ng two
functi onal 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
⍺ - amino acids

amino
groups – attached to
the
carboxyl same carbon Atom

⍺ - 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
3. Polar AA with (+) ‘R’ group

• carries (+) charge


• Examples:
Histidine Arginine
Lysine

4. Polar AA with (-) ‘R’ group

• carries (-) charge


• Examples:
Glutamic Acid Aspartic
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
  

- 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 - held by
an
COOH ⍺-
carbon
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

H C OH OH C
H

CH2OH CH2OH

D-Glyceraldehyde L-
R R

H C NH2 H2N
C H

COOH COOH

D-Amino Acid
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 dipo la r 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 H NH2
Cation H໋ H໋ Anion
(low pH) R C COO ¯ (high
pH)
Isoelectric pH (symbol pI)

–      
      
   

   
Calculation of the pI value

–     
 
   

    
   

  
     ໋
 

   
   
Leucine

–      
 
    

       

   
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
R CH
COO¯
R CH2 + CO2

NH3໋

NH3໋

this reaction
assumes
3. Reaction with Ammonia

- the carboxyl group of


dicarboxylic AA reacts with
NH3 to form amide

Asparatic Acid + NH3 


Asparagine
Glutamic Acid + NH3 
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 (Ruhemann’s
purple)
Amino acid + Ninhydrin  Keto
acid + NH3 + CO2
+ Hydrindantin

Hydrindantin + NH3 + Ninhydrin


 Ruhemman’s
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
• Buiret Reaction Two peptide linkages
• Ninhydrin Reaction ⍺-Amino acids
• Xanthoproteic Reaction Benzene ring of
aromatic AA (Phe, Tyr,
Trp)
• Million’s reaction Phenolic Group (Tyr)
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