Amino acids

For MLS student 2021

Batches: 2 and 3
By: Dr. Adam Osman Abaker
Structural Feature of Proteins
Proteins functionally diverse molecules in living
systems such as:
 Enzymes and polypeptide hormones.
 Myosin, a contractile protein of muscle.
 Bone, consisted from the protein collagen.
 Blood proteins, such as hemoglobin and
plasma albumin and immunoglobulins.
All share the common structural feature of being
linear polymers of amino acids
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 Introduction to amino acids
•Amino acids are building blocks of proteins.
•Proteins are composed of 20 different amino acids (encoded
by standard genetic code, construct proteins in all species ).

•Their molecules containing both amino and carboxyl

groups attached to the same a-carbon (L-a-amino acids).

•Their chemical structure influences three dimensional

structure of proteins.
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Intro. To amino acids cont.
•They are important intermediates in metabolism
(porphyrins, purines, pyrimidines, keratin, urea …
etc).

•They can have hormonal and catalytic function.

•Several genetic disorders are cause in amino acid
metabolism errors (aminoaciduria - presence of
amino acids in urine)

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Structure of the amino acids
Each amino acid (except for proline) has:
1. A carboxyl group (-COO-) .
2. An amino group (-NH3+) .
3. Side chain ("R-group") bonded to the α-carbon
atom.
4. α-Hydrogen.
These carboxyl and amino groups able to combine in
peptide linkage between 2 a.a. forming a
polypeptide.
In case of proline, the side chain is linked with the alpha
amino group forming cyclic form.
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Optical Properties of
Amino Acids
 The α-carbon of a.a.
is attached to four different
chemical groups as chiral or
optically active carbon atom.
 Glycine is the exception.
 Amino acids exist in two
forms, D and L, that are
mirror images of each other.
 All amino acids found in
proteins are of the L-
configuration.
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Nonionic and zwitterion forms of amino acids

Zwitterion = in German for „hybrid

ion“

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Classification of Amino acids
They are classified according to the side chain:
Amino acids with nonpolar side chains.
Aromatic R Groups.
Amino acids with uncharged polar side
chains.
Positively Charged (Basic) R Groups.
Amino acids with acidic side chains.

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 Nonpolar (Hydrophobic) R Groups
Glycine (Gly)

Alanine (Ala)

Valine (Val)

Leucine (Leu)

Isoleucine (Ile)
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Alanine, Valine, Leucine and Isoleucine have saturated
hydrocarbon R groups (i.e. they only have hydrogen and
carbon linked by single covalent bonds).  Leucine and
Isoleucine are isomers of each other.

Alanine Valine

Leucine Isoleucine
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The side chain of Methionine includes a sulfur atom
but remains hydrophobic in nature. 

Phenylalanine is Alanine with an extra benzene

(sometimes called a Phenyl) group on the end. 
Phenylalanine is highly hydrophobic and is found
buried within globular proteins. 

Methionine Phenylalanine

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Tryptophan is highly hydrophobic and tends to be found
immersed inside globular proteins. 

Structurally related to Alanine, but with a two ring

(bicyclic) indole group added in place of the single aromatic
ring found in Phenylalanine. 

The presence of the nitrogen group makes Tryptophan a

little less hydrophobic than Phenylalanine.

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Proline is unique amongst the amino acids – its
side chain is bonded to the backbone nitrogen as
well as to the a-carbon. 

Because of this proline is technically an imino

rather than an amino acid. 

The ring is not reactive, but it does restrict the

geometry of the backbone chain in any protein
where it is present.  

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Polar (Hydrophilic) R Groups

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Tyrosine is Phenylalanine with an extra hydroxyl (-OH) group
attached. 
It is polar and very weakly acidic.  Tyrosine can play an
important catalytic role in the active site of some enzymes.
Reversible phosphorylation of –OH group in some enzymes is
important in the regulation of  metabolic pathways

Serine and Threonine play important role in enzymes

which regulate phosphorylation and energy metabolism.

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Cysteine has sulfur-containing side group.The group has the
potential to be more reactive. It is not very polar.

Cysteine is most important for its ability to link to another

cysteine via the sulfur atoms to form a covalent disulfide
bridge, important in the formation and maintenance of the
tertiary (folded) structure in many proteins.

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Asparagine and Glutamine are the amide derivatives
of Aspartate (Aspartic acid) and Glutamate
(Glutamic acid) - see below.  They cannot be ionised
and are therefore uncharged. 

Asparagine Glutamine

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Negatively (polar) Charged R Groups

Two amino acids with negatively charged (i.e. acidic) side

chains - Aspartate (Aspartic acid) and Glutamate (Glutamic
acid). 

These amino acids confer a negative charge on the proteins of

which they are part. 

Aspartic acid (Asp)

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 Positively Charged R Groups
Lysine and Arginine both have pKs around 10.0 and are
therefore always positively charged at neutral pH. 
With a pK of 6.5, Histidine can be uncharged or positively
charged depending upon its local environment. 
Histidine has an important role in the catalytic mechanism of
enzymes and explains why it is often found in the active site.

Lysine (Lys) Arginine (Arg) Histidine (His)

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 Classification Based on Chemical
Constitution
Small amino acids – Glycine, Alanine
Branched amino acids – Valine, Leucine, Isoleucine
Hydroxy amino acids (-OH group) – Serine, Threonine
Sulfur amino acids – Cysteine, Methionine
Aromatic amino acids – Phenylalanine, Tyrosine, Tryptophan
Acidic amino acids and their derivatives – Aspartate,
Asparagine, Glutamate, Glutamine
Basic amino acids – Lysine, Arginine, Histidine
Imino acid - Proline
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Essential Amino Acids in Humans
• Required in diet.
• Humans incapable of forming requisite
carbon skeleton.

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Non-Essential Amino Acids in Humans

Not required in diet

Can be formed from a-keto acids by
transamination and subsequent reactions

* Essential amino acids

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The two stereoisomers of alanine

Two stereoisomers are called

enantiomers.

The solid wedge-shaped bonds

project out of the plane of paper,
the dashed bonds behind it.

The horizontal bonds project out of

the plane of paper, the vertical bonds
behind.

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 Uncommon Amino Acids
Hydroxylysine and hydroxyproline, are found
in the collagen and gelatin proteins.
Thyroxin and 3,3`,5-triiodothyronine,
iodinated a. a. are found in thyroglobulin, a
protein produced by the thyroid gland.
γ-Carboxyglutamic acid is involved in blood
clotting.
Finally, N-methylarginine and N-acetyllysine
are found in histone proteins associated with
chromosomes.

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Intermediates of biosynthesis of
arginin and in urea cycle

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 ACIDIC AND BASIC PROPERTIES OF
AMINO ACIDS
Amino acids in aqueous solution contain weakly
acidic α-carboxyl groups and weakly basic α-
amino groups.
 Each of the acidic and basic amino acids contains
an ionizable group in its side chain.
 Thus, both free and some of the combined amino
acids in peptide linkages can act as buffers.
The concentration of a weak acid (HA) and its
conjugate base(A-) is described by the Henderson-
Hasselbalch equation.
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Derivation of the equation
For the reaction (HA A- + H+ )
[H+] [A-]
Ka = ───── ------ (1)
[HA]
 By solving for the [H+] in the above equation.
 taking the logarithm of both sides of the equation.
and multiplying both sides of the equation by -1
 then substituting
 pH = -log [H+] and pKa = -log [Ka] we obtain:
[A-]
pH = pKa + log ─── ------ (2)
[HA]
It is the (Henderson-Hasselbalch equation)
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Buffers

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Titration Solution of an amino acid

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Titration curve of glycine

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Other applications of the Henderson-Hasselbalch
equation

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 Ninhydrin Reaction

This strong oxidizing agent

bring about the oxidative
decarboxylation of amino
acid. The ammonia and
hydrindant in formed
ninhydrin, a purple pigment.

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Peptide Bond Formation

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Thank You

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