Amino acids structure

Amino Acids Structure
&
Properties
By
Dr. Narottam Agrawal
Faculty, Rajkiya Medical College Jalaun (Orai),
U.P. INDIA

Specific Learning Objectives (SLO)
 General structure of amino acid
 Amino acid as Ampholytes (acid and base),
Zwitter ions.
 Classification of amino acid on the basis of side
chain, chemical composition, Nutritional
Requirement and metabolic fate.
 Derived amino acids.
 Optical properties of amino acids.
 Acid-Base properties and Buffer characteristic.
 Biological Important Peptides
 Proteins based on nutritional value

STRUCTURE OF THE AMINO ACID
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.
 Carboxyl group of one
amino acid joined
together with amino
group of second amino
acid by peptide linkage
and a dipeptide is
formed.

Nonionic and zwitterion forms of amino acids
The zwitterion predominates at neutral pH
Week acid
Week base

Classification of Amino Acids on
the basis of side chains
Amino acids varies in their side chains, that’s why
they are classified on the basis of their side chain.
Amino acids are divided in to five groups. They are-
 Amino acids with nonpolar aliphatic side chains.
 Amino acids with Aromatic R Group.
 Amino acids with uncharged polar side chains.
 Amino acids with Positively Charged R Groups (Basic
amino acids).
 Amino acids with Negatively charged R Groups (Acidic
amino acids).

Amino acids with nonpolar aliphatic
side chains

Amino acids with nonpolar aliphatic side chains
• The side chains of amino acids cluster in the
interior of the protein due to hydrophobicity.
• The side chain of proline and its α-amino group
form a ring structure.
• Proline gives the fibrous structure of collagen,
and interrupts the α-helices found in globular
proteins.

Amino acids with Aromatic (R) Groups
 Their aromatic side chains, are nonpolar so that they
participate in hydrophobic interactions.
 Tyrosine is an important in some enzymes.
 Most proteins absorb light at a wavelength of 280 nm due to
aromatic groups.

Absorption Spectra of Aromatic
Amino Acids
This property
exploited by
researchers in the
characterization of
proteins.

Amino acids with uncharged polar side chains
More hydrophilic
because they
form hydrogen
bonds with water.
They are serine,
threonine,
cysteine,
asparagine, and
glutamine.

• Cysteine contains a sulfhydryl group (-SH), an important
component of the active site of many enzymes.
• Two cysteines can become oxidized to form a dimmer cystine, which
contains a covalent cross-link called a disulfide bond (-S-S-).
• Serine and threonine contain a polar hydroxyl group. This group
serve as a site of attachment (in enzymes) for groups such as a
phosphate.
• Amide group of asparagine, as well as the hydroxyl group of serine
or threonine serve as a site of attachment for oligosaccharide chains
in glycoproteins.
Amino acids with uncharged polar side chains

Amino acids with positively charged R
Groups (Basic Amino acid)
• The R groups have
significant positive charge.
• Lysine has a second positive
amino group at the ε position
on its (R) chain.
• Arginine has a positively
charged guanidino group.
• Histidine has a positive
imidazole group facilitates
the enzyme-catalyzed
reaction by serving as a
proton donor/acceptor.

Amino acids with Acidic Side Chains
Aspartic and glutamic
acid are proton donors.
At neutral pH, the side
chains of these amino
acids are fully ionized.
At low pH, the side
chains of these amino
acids are fully protonated.
They have a negatively
charged carboxylate
group (-COO-) at
physiologic pH.

Derived Amino Acids found in proteins
• 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.
• N-methylarginine and N-acetyllysine are found in
histone proteins associated with chromosomes.
• Desmosine found in elastin , a protein of comnnective
tissue such as skin, lungs and elastic arteries
.

Derived amino acids found in proteins

Classification Based on Chemical Composition
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

• Required in diet
• Humans incapable of forming requisite carbon skeleton
(FILTH RKM VW)
Arginine*
Histidine*
Isoleucine
Leucine
Valine
Lysine
Methionine
Threonine
Phenylalanine
Tryptophan
* Essential in children, not in adults
Essential Amino Acids in Humans

Amino acid based on Metabolic Fate
On the basis of their end products amino acids are following
types:-
• Ketogenic amino acids: They are degraded to Acetyl Co A or
Acetoacetyl Co A. eg: Leucine and lysine
• Ketogenic and glucogenic amino acids : eg: Tryptophan,
Isoleucine, phenylalanine and tyrosine (WIFY).
• Glucogenic amino acids : There are degraded to pyruvate, α-
ketoglutarate, succinyl-coA, fumarate or oxalloacetate.
Eg: Rest of the amino acids
 All these intermediate products enter in to citric acid cycle and
used for –
- Synthesis of glucose
- Synthesis of lipid
- Production of energy and converted in to CO2 and H2O

Optical Properties of Amino Acids
• The α-carbon of a.a.
is attached to four
different chemical
groups is a chiral or
optically active carbon atom.
• With the exception of Glycine, all the amino acids are optically
active.
• Amino acids, those rotate the plane polarized light in clock wise
direction, called as dextrorotatory (d isomer), and those rotate in
anticlock wise direction called as levorotatory (l isomer).
• 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.

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.

Derivation of the equation
• For the reaction (HA H+ + A- )
[H+] [A-]
• Ka = ───── ------ (1)
[HA]
• By solving for the [H+] in the above equation,
taking the logarithm of both sides of the
equation, multiplying both sides of the equation
by -1, and substituting pH = -log [H+] and pKa
= -log [Ka] we obtain:
[A-]
• pH = pKa + log ─── ------ (2)
[HA]
It is the (Henderson-Hasselbalch equation)

Protonated form Unprotonated form (conjugate base)
HA H+ A-
+
Ka
[HA]
[H+] [A-]
=
= Ka x
[A-]
[HA]
[H+]
-log
[H+]
-log Ka
-log
[A-]
[HA]
=
pH = pKa log
[A-]
[HA]
+
Henderson/Hasselbach equation and pKa

Titration of an amino acid
At Isoelectric point Zwitter ion is found which has net Charge Zero

Titration curve of Acidic Amino acid: Glutamate

Titration curve of Basic Amino acid: Histidine

Biologically Important Peptides
Some oligopeptides have biological importance
these are-
Thyrotropin releasing hormone (TRH):- made up of
tripeptide (Glu-His-Pro) released from hypothalamus and act on
ant. Pituitary for release of thyrotropin (TSH) and prolactin.
Glutathione :- It is a tripeptide Gammaglutamyl-cysteinyl-glycine,
involve in RBC membrane integrity and important for keeping
enzyme in active state.
Enkephalin: Pentapeptide, act as neurotransmitter in brain.
Oxytocin & Vasopressin (ADH):- Both are nanopeptides secreted by
posterior pituitary
Angiotensin :- Angiotensin I contain 10 amino acids and Angiotensin
II has 8 amino acids they increase blood pressure.

Protein based on Nutrition value
Nutrionally Rich Proteins:- They are complete proteins or
first class proteins. Contains all the essential amino acids in the
required proportion. On supplying these protein in diet, children will
grow satisfactorily (eg. Casein of milk)
Incomplete protein :- They lack one essential amino acid. They can
not promote body growth in children but may be able to sustain
body weight in adults. (eg. proteins from pulses are lack of
methionine, protein of cereals lack in lysine , but combination of
both adequate growth may be obtained.
Poor Proteins :- They lack in many essential amino acids and diet
based on these protein will not sustain the original body weight
(Zein from corn lacks Tryptophan and Lysin )

Summary
• The 20 amino acids commonly found as residues in proteins
contain an α-carboxyl group, an α-amino group, and a distinctive
R group substituted on the α-carbon atom.
• The α-carbon atom of all amino acids except glycine is
asymmetric, and thus amino acids can exist in at least two
stereoisomeric forms.
• Only the L stereoisomers, are found in proteins, Since active site
of enzymes are assymetric so they produce L-AMINO ACIDS.
• Amino acids are classified into five types on the basis of the
polarity and charge (at pH 7) of their R groups.
• Amino acids vary in their acid-base properties and have
characteristic titration curves. Monoamino monocarboxylic
amino acids (with nonionizable R groups) are diprotic acids
(+H3NCH(R)COOH) at low pH and exist in several different
ionic forms as the pH is increased. Amino acids with ionizable R
groups have additional ionic species, depending on the pH of the
medium and the pKa of the R group.

Amino acids structure

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