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 R C NH2 COOH R H C NH3 COOH

General Structure

_⍺ - amino acids amino

the attached to same carbon Atom

groups –

carboxyl

⍺ - 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 Leucine Isoleucine Valine Methionine Phenylalanine
Tryptophan Proline

_3. Polar AA with (+) ‘R’ group • carries (+) charge • Examples: Histidine
Lysine

Arginine

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 an carbon

R H COOH
- 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 H H CH2OH D-Glyceraldehyde CH2OH LC OH OH C

_R H C NH2

R H2N

COOH D-Amino Acid L-Amino Acid

COOH

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

H R C COO ¯ NH3໋ Cation (low pH) pH) COOH

NH2 Amino Acid R

H C

H H໋ R C H໋ COO ¯ Anion

NH2 (high

_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 NH3
to form amide Asparatic Acid + NH3 Asparagine Glutamic Acid + NH3

with

_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 group or AA
• • • • Buiret Reaction Ninhydrin Reaction Xanthoproteic Reaction Million’s
reaction

Specific
Two peptide linkages ⍺-Amino acids Benzene ring of aromatic AA (Phe, Tyr,
Trp) 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

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