BIOCHEMISTRY

AMINO ACIDS
PEPTIDS and PROTEINS
 AGENDA:
AMINO ACIDS – essencial, non essencial
PROTEINS – structure: primary,
secondary, tertiary and quaternary
physical and chemical properties;
simple proteins;
proteinogramm
compaund proteins
chromoproteins, citochroms,
lipoproteins α- β- preβ- khilomicrons
metaloproteins
All proteins, which may find in living bodies, are
consists of amino acids

Degradation of proteins into smaller fragments –

polypeptide chains may be broken by
proteolytic enzymes such as trypsin,
chymopripsin, pepsin, elastase – the final point
of protein degradation is amino acid.
All amino acids occur in proteins
are L-, and α- (alpha)- amino acids
Electrophoresis (electrophoregram)
 Classification of Amino Acids

A.Classification based on structure:

Each amino acid is assigned a 3 letter or 1 letter
symbol
These symbols are commonly used to represent
the amino acids in protein structure
e.g.:
ANGIOTENSIN II (octapeptide)
[Asp-Arg-Val-Tyr-Ile-His-Pro-Phe]
or simply
[D-R-V-Y-I-H-P-F]
Glycine
Alanine
Phenilalanaine
Cystein
Methionine
Valine
Leucine
Isoleucine
Tyrosine
Arginine
Glutamate
Proline
Tryptophan
 Classification of amino acids based on polarity

There are four groups of AA depending to polarity

1.Non-polar AA (also referred as hydrophobic [water hating]) no charge
on ‘R’ group
[Alanine, Leucine, Isoleucine, Valine, Methionine, Phenylalanine,
Tryptophan, Proline]
2.Polar AA with no charge on ‘R’ group
[Glycine, Serine, Threonine, Cysteine, Glutamine, Asparagine.
Tyrosine]
– they however possess groups such as hydroxyl, sulfhydryl, amide –
and participate in hydrogen bonding of protein structure.
3.Polar AA with positive ‘R’ group
[Lysine, Arginine, Histidine]
4.Polar AA with negative ‘R’
group [Aspartic acid, Glutamic
Acid]
 20
Amino
Acids
 Amino
Acids
non-polar,
aliphatic
Aromatic
Amino
Acids
Positively
charged
Amino
Acids
Negatively
charged
Amino
Acids
 Polar,
ancharged
Amino
Acids
Amino Acids found in proteins are also can be
divided into seven distinct groups

-AA with aliphatic side chains

-Hydroxyl group containing AA

-Sulfur containing AA

-Acidic AA and their amides

-Basic AA

-Aromatic AA

-Imino acids
 Aliphatic amino acids

[Glycin, Alanin, Valin, Leucin, Isoleucin]

Hydroxyl group containing AA

[Serine, Threonine, Tyrosine]

 Sulfur containing AA
[Cystein (with sulfhydryl group), Methionine (with thioether
group)]
 Acidic Amino acids and their amides

[Aspertic acid (Aspartate), Glutamic acid (Glutamate)] – dicarboxylic

monoamino acids
[Aspargine, Glutamine] – their respective amide derivatives
all these four AA possess distinct codons for their incorporation
into proteins
Basic AA

[Lysine, Arginine (with gunidino

group), histidine (imidazole ring)]
dibasic monocarboxylic acids (they
are highly basic in character)
 Aromatic AA
[Phenilalanine, Tyrosine, Tryptophan (with indole ring)]
 Imino acids

[Proline (containing pyrrolidine ring)] – it has an imino group (=NH)

instead of amino group (–NH2). Therefore Proline is α-imino acid
Diamino amino acids
monoamino-monocarboxylic amino acids
monoamino-dicarboxylic amino acids
monoamino-dicarboxylic amino acids
diamino monocarboxylic amino acids
 heterocyclic amino acids

Histidine, Tryptophan, Proline – can be considered as heterocyclic

AA
 Amino
Acids
variant of
classification
 Nutrificational classification of amino acids

The 20 AA are required for the synthesis of variety proteins,

besides other biologicalfunctions.
However, all these 20 AA need not be taken in the diet.

Based on the nutritional requirements, amino acids are grouped into

two classes:
Essential and Non-essential.
 Essential and non-essential amino acids
The AA which are cannot be synthesized by the body, and therefore, need to be
supplied through the diet are called essential AA.
They are required for proper growth and maintanance of the individual.
Arginine
Valine
Histidine
Isoleucine
Leucine
Methionine
Phenylalanine
Threonine
Tryptophan
Arginine and Histidine can be synthesized by adults and not by growing children
they are considered as semi-essential AA.
Thus 8 AA absolutely essential while 2 are semi-essential.

Non-essential (or dispensable) AA:

Glycine, Alanine, Serine, Cysteine, Aspartate, Asparagine, Glutamate, Glutamine,
Tyrosine, Proline.
 AA classification based on their metabolic fate

Carbone skeleton of AA can serve as a precursor for the synthesis

of glucose (glycogenic) or fat (ketogenic) or both.

1.Glycogenic AA (can serve as precursors for the formation of glucose

or glycogen)
[Alanine, Aspartate, Glycin, Methionine etc]

2.Ketonic AA (fat can be synthesized)

[Leucine, Lysine]

3.Glycogenic and kethogenic AA

[Isoleucine, Phenylalanine, Tryptophan, Tyrosine] – precursors for
synthesis of glucose as well as fat.
 I.Physical propertie of amino acids1-solubility

1.Solubility
– most of amino acids are usually soluble in water and insoluble in
organic solvents
 I.Physical properties of amino acids2-melting

2.Melting point
– amibno acids generally melt at higher temperature, often above 200ºC
 I.Physical properties of amino acids3-taste

3.Taste
– amino acids may be
-sweet (Gly, Ala, Val),
-tasteless (Leu),
-bitter (Arg, Ile)
Monosodium glutamate (MSG, ajinomoto) is used as a flavoring agent in
food industry, and Chinese food to increase taste and flavor.

In some individuals intolerant to Monosodium glutamate (MSG),

Chinese syndrome (brief and reversible flulike symptoms) is observed.
 I.Physical properties of amino acids4-optical

4.Optical properties – all amino acids (except Glycine)

possess optical isomers
due to the presence of asymmetric carbon atom
D- (right rotating) and L- (left rotating)-forms
of amino acid
(based on the structure of glyceraldehyde)
 I.Physical properties of amino acids5-ampholytes
Amiono acids as ampholytes
AA contain both acidic (–COOH) and basic (–NH2) groups.
They can donate a proton or accept a proton – hence AA are regarded as
ampholytes.

Zwitter ion (or dipolar ion) – [name zwitter is from German –

means hybrid].
Is a hybrid molecule containing positive and negative ionic groups.

The AA rarely exist in a neutral form with free carboxylic (–COOH)

and free amino [basic] (–NH2) groups. In strongly acidic pH (low pH),
the amino acid is positively charged (cation), while in strongly alkaline
pH (high pH), it is negatively charged (anion). Each AA has a
characteristic pH at which it carries positive and negative charges and
exists as zwitterions.
General structure of amino acid and its ion form
Existence of an amino scid as anion and
zwitterion
 I.Physical properties of amino acids5-isoelectricity

Isoelectric pH (sympol pI) is difined as the pH at which a

molecule exists as a zwitterions or dopolar ion and carries no
net charge. Thus, the molecule is electrically neutral.
The pI value can be calculated by taking the average pKa
values corresponding to the ionizable groups.
Titration curve of amino acid [Leucine]
 II1.Chemical properties of amino acids

Amino acids with their acidic part form salts with bases
(e.g. with NaOH forming compouns like R–COONa)
and in reactions with alcohols they form esters (–
COOR´)
 II2. Chemical properties of amino acids

Amino acids undergo decarboxylation – to produce

corresponding amines

Reactions due to –COOH group

this reaction assumes significance in the living cells due to the
formation of many biologically important amines [histamine
(from histidine), tyramine (from tyrosine), γ-amino buteric
acid (GABA) – from grutamate]
 II3. Chemical properties of amino acids

Reaction with ammonia

carboxyl group of dicarboxylic acids reacts with NH3 to form
amide

Aspartic acid + NH3 → Asparagine

Glutamic acid + NH3 → Glutamine

Reactions due to – NH2 group

 II4. Chemical properties of amino acids

The amino group behave as base and combine

+
with acids (e.g
–
HCl) to forn salts (–NH3 Cl )
II5. Chemical properties of amino acids
Colour reactions of proteins/amino
acids – are used to identified amino acids
 II6. Chemical properties of amino acids

Reaction with ninhydrin.

The α-amino acids react with ninhydrine to form a purple,
blue, or pink colour complex (Ruhemann’s purple)
This reaction used for the quantative determination of
amino
acids and protein.
NB Proline and Hydroxyproline give yellow colour with
ninhydrine.
 II7. Chemical properties of amino acids

Transamination – very important reaction in amino acid

metabolism – based on transfer of an amino group from an
amino acid to keto acid to form a new amino acid
 II8. Chemical properties of amino acids

Amino acid in reaction of oxidative deamination – liberate

free ammonia
 Amino acids used in Drugs

D-Penicillamine (D-dimethylglycine)
N-Acetylcysteine
Gabapentine (γ-amonobutyrate linked to
cyclohexane)
Formation of a peptide bonds
Peptide bond
 Dimensions of a fully extended polypeptide
chain
(the distance between two adjacent alfa-carbon atoms is 0.36 nm)
 Classification of peptides and proteins

Peptides names consist af amino acids and always

start with amino ending amino acid listing the
sequence of all next

Peptides are divided into oligopeptide (40 and less

amino acind)
and polypeptides – more than 40 amino acids
 Structure of proteins

Primary structure of protein

Secondary structure of

protein

Tertiary structure of proteins

 Protein structure
(primary, secondary, tertiary, quaternary)
Secondary structure of
protein

A right handed alfa-helix

–CH–R groups of amino
acids; Dotted blue lines are
hydrogen bonds.

[here only a few hydrogen bonds shown

for clarity]
Denaturation of protein
Classification of proteins
 Functional classification of
proteins 1.Structural proteins
(keratin, collagen)
3. Transport proteins (hemoglobin, serum albumin)
2.Enzymes (or catalytic) proteins
4. Hormonal(pepsin,
proteins (insulin, growth
hexokinase)
hormone) 5.Contractile proteins (actin,
myosin) 6.Storage proteins (ovalbumin,
glutelin)
7.Genetic proteins (nucleoproteins)
8.Defense proteins (immunoglobulins, snake
venoms)
 Protein classification based on chemical nature
and solubility

1.Simple proteins (only AA residues)

2.Conjugated proteins(plus non protein

moiety – prosthetic group)

3.Derived proteins – degraded ordenaturated

products of simple and conjugated proteins
Thank YOU for ATTENTION