Pharmaceutical

Chemistry II
Biochemistry
Muhammad Wajid Pharm-D, M.Phil., Ph. D Scholar
(Pharmaceutical Chemistry)
Assistant Professor Gulab Devi Institute of Pharmacy,
GDEC, Lahore
 Chemistry of
Protein

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Muhammad Wajid
Assistant Professor of Pharmaceutical Chemistry, Gulab Devi Institute of Pharmacy, Lahore
 Protein:

The term protein is derived from a Greek word proteios meaning “holding the first place”.
Berzelius (Swedish chemist) suggested the name proteins to the group of organic compounds
that are utmost important to life. Mulder (Dutch chemist) in 1838 used the term proteins for
the high molecular weight nitrogen-rich and most abundant substances present in animals and
plant.

Proteins are organic compounds with a high molecular weight formed of carbon, oxygen,
hydrogen and nitrogen and may also contain sulfur, phosphorus coloring non-protein organic
groups and metal ions.

Composition of proteins:

Proteins are predominantly constituted by five major elements in the following proportions

o Carbon : 50-55%
o Hydrogen : 6-7.3%
o Oxygen : 19-24%
o Nitrogen : 13-19%
o Sulfur : 0-4%

Major elements

o C, H, O, N, S

Trace elements

o P, Fe, Cu, Zn, I

The average nitrogen content in proteins is about 16%.

Functions of proteins:

Proteins perform a great variety of specialized and essential functions in the living cells.
These functions may be broadly grouped as static (structural) and dynamic.

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Muhammad Wajid
Assistant Professor of Pharmaceutical Chemistry, Gulab Devi Institute of Pharmacy, Lahore
 Structural functions:

Certain proteins perform brick and mortar roles and are primarily responsible for structure
and strength of body. These include collagen and elastin found in bone matrix, vascular
system and other organs and α-keratin present in epidermal tissues.

Dynamic functions:

The dynamic functions of proteins are more diversified in nature. They include:

o Biochemical catalysts known as enzymes are proteins

o Proteins known as immunoglobulins serve as the first line of defence against
bacterial and viral infections
o Several hormones are protein in nature
o Some proteins present in cell membrane, cytoplasm and nucleus of the cell act as
receptors
o The transport proteins carry out the function of transporting specific substances
either across the membrane or in the body fluids
o Storage proteins bind with specific substances and store them e.g. iron is stored as
ferritin.
Amino Acids:

Amino acids are organic acids that contain -NH2 group. All these amino acids are alpha-
amino acids means that the amino group is attached to the -carbon atom.

OR

Amino acids are a group of organic compounds containing two functional groups amino and
carboxyl. The amino group (-NH2) is basic while the carboxyl group (-COOH) is acidic in
nature. The α-carbon atom binds to a side chain represented by R which is different for each
of the 20 amino acids found in proteins. The amino acids mostly exist in the ionized form in
the biological system. R

H2N C H

COOH

-L-Amino acid
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Muhammad Wajid
Assistant Professor of Pharmaceutical Chemistry, Gulab Devi Institute of Pharmacy, Lahore
Each amino acid (except proline and hydroxyproline) has a carboxyl group (-COOH), an
amino group (-NH2) and a characteristic side chain (R).

All amino acids (except glycine) are optically active i.e. can rotate plane polarized light. This
is because the 4 groups attached to -carbons are different. In glycine, the -carbon is
attached to 2 hydrogen atoms, therefore, is optically inactive.

Selenocysteine 21st L-α- Amino acid:

Selenocysteine is an L-α-amino acid found in protein in every domain of life. Selenocysteine

is an unusual amino acid containing the trace element selenium in place of sulfur atom of
cysteine. Selenocysteine occurs at the “active site” of several enzymes. Human contain about
two dozen selenoprotein. Selenoprotein is responsible for converting prohormone thyroxin
(T4) to thyroid hormone 3, 3′ 5-triiodothyronine (T3). Incorporation of selenocysteine into the
proteins during translation is carried out by the codon namely UGA. It is interesting to note
that UGA is normally a stop codon that terminates protein biosynthesis.
H
H2 C C COO

SeH NH3

Selenocysteine
Pyrrolysine 22nd amino acid:
In the year 2002, some researchers have described yet another amino acid namely pyrrolysine
as the 22nd amino acid present in protein. The stop codon UAG can code for pyrrolysin.
Zwitterion:

The Zwitter is derived from the German word which means hybrid. Zwitter ion (or dipolar
ion) is a hybrid molecule containing positive and negative ionic groups. The amino acids
rarely exist in a neutral form with free carboxylic (-COOH) and free amino (-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 amino acid has a characteristic
pH (e.g. leucine, pH 6.0) at which it carries both positive and negative charges and exists as
zwitterion.

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Muhammad Wajid
Assistant Professor of Pharmaceutical Chemistry, Gulab Devi Institute of Pharmacy, Lahore
 H

R C COO

NH3

Zwitterion

Isoelectric pH:

Isoelectric pH (symbol pl) is defined as the pH at which a molecule exists as a zwitterion or

dipolar ion and carries no net charge. Thus, the molecule is electrically neutral.

Leucine exists as cation at pH below 6 and anion at pH above 6. At the isoelectric pH (pl =
6.0), leucine is found as zwitterion. Thus the pH of the medium determines the ionic nature of
amino acid.

Low pH R

H C NH3

COOH

Cation
R

H C NH3
Zwitterion
COO
Isoelectric pH

H C NH2
High pH
COO

Anion

Classification of amino acids:

There are different ways of classifying the amino acids based on the structure and chemical
nature, nutritional requirement, metabolic fate etc.

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Muhammad Wajid
Assistant Professor of Pharmaceutical Chemistry, Gulab Devi Institute of Pharmacy, Lahore
 Amino acid classification based on the structure:

Amino acids can be classified into 6 groups depending on their structure. They include:

o Amino acids with aliphatic side chain

o Amino acids containing hydroxyl (-OH) group
o Sulfur containing amino acid
o Acidic amino acids and their amides
o Basic amino acids
o Aromatic amino acids
o Imino acid
Amino acids with aliphatic side chain:

These are monoamino monocarboxylic acids. This group consists of the most
simple amino acids-glycine, alanine, valine, leucine and isoleucine. Valine, leucine and
isoleucine contain branched aliphatic side chains; hence they are referred to as branched
chain amino acid.

H H

H C NH2 H3C C NH2

COOH COOH

Glycine
Alanine

H3C H H3C H
H2
CH C NH2 CH C C NH2
H3C H3C
COOH COOH

Valine Lecine

H3C

CH2 H

CH C NH2
H3C
COOH

Isolecine

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Muhammad Wajid
Assistant Professor of Pharmaceutical Chemistry, Gulab Devi Institute of Pharmacy, Lahore
 Hydroxyl group containing amino acids:

Serine, threonine and tyrosine are hydroxyl group containing amino acids.
Tyrosine-being aromatic in nature is usually considered under aromatic amino acid.

H H
H
H2C C NH2 HO C C NH2

OH COOH OH COOH

Serine Threonine

Sulfur containing amino acid:

Cysteine with sulfhydryl group and methionine with thioether group are the two amino acids
incorporated during the course of protein synthesis. Cystine, another important sulfur
containing amino acid, is formed by condensation of two molecules of cysteine.

H H

H2C C NH2 H 2C C NH2

SH COOH S COOH

S H
Cysteine
H 2C C NH2

COOH

Cystine

H
H2
H2C C C NH2

S COOH

CH3

Methionine

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Muhammad Wajid
Assistant Professor of Pharmaceutical Chemistry, Gulab Devi Institute of Pharmacy, Lahore
 Acidic amino acids and their amide:

Aspartic acid and glutamic acids are dicarboxylic monoamino acids while asparagine and
glutamine are their respective amide derivatives.

H H

H2 H2
HOOC C C NH2 H2N C C C NH2

COOH O COOH

Aspartic acid Asparagine

H H
H2 H2 H2 H2
HOOC C C C NH2 H2N C C C C NH2

COOH O COOH

Glutamine
Glutamic acid

Basic amino acid:

The three amino acids lysine, arginine (with guanidino group) and histidine (with imidazole
ring) are dibasic monocarboxylic acid.
H
H2 H2 H2 H2
H2N C C C C C NH2

COOH

H Lysine
H2
C C NH2
H
HN N COOH H2 H2 H2
HN C C C C NH2

C NH
Histidine
NH2 8
Arginine
Muhammad Wajid
Assistant Professor of Pharmaceutical Chemistry, Gulab Devi Institute of Pharmacy, Lahore
 Aromatic amino acids:

Phenylalanine, tyrosine and tryptophan (with indole ring) are aromatic amino acid.

H H
H2 H2
C C NH2 HO C C NH2

COOH COOH

Phenylalanine Tyrosine

H
H2
C C NH2

COOH
N
H

Tryptophan

Imino acids:

Proline containing pyrrolidine ring is a unique amino acid. It has an imino group (=NH),
instead of an amino group (-NH2) found in other amino acids. Therefore, proline is an imino
acid.

COOH
N
H

Proline

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Muhammad Wajid
Assistant Professor of Pharmaceutical Chemistry, Gulab Devi Institute of Pharmacy, Lahore
 Nutritional classification of amino acids:

The twenty amino acids are required for the synthesis of variety of proteins, besides other
biological functions. However, all these 20 amino acids need not be taken in the diet. Based
on the nutritional requirements, amino acids are grouped into three classes:

o Essential amino acids:

o Non-essential amino acids
o Semi-essential amino acids
Essential amino acids:

The amino acids which cannot be synthesized by the body and, therefore, need to be supplied
through the diet are called essential amino acids. They are required for proper growth and
maintenance of the individual. Otherwise their deficiency will lead to a nutrition deficiency
disease that affects both growth and health. They include valine, leucine, isoleucine,
phenylalanine, threonine, tryptophan, methionine and lysine. Eight amino acids are generally
regarded as essential for humans. Two others, histidine and arginine are essential only in
children. A good mnemonic device for remembering these is "Private Tim Hall", abbreviated
as:

PVT TIM HALL

Non-essential or dispensable amino acids:

The body can synthesize about 10 amino acids to meet the biological needs; hence they need
not be consumed in the diet. These are glycine, alanine, serine, cysteine, aspartate,
asparagine, glutamate, glutamine, tyrosine and proline.

Semi-essential amino acids:

These are growth promoting factors since they are not synthesised in sufficient quantity
during growth. They include arginine and histidine. They become essential in growing
children, pregnancy and lactating women.

Classification Based on the Fate of Each Amino acid:

Amino acids can be classified here as Glucogenic (potentially be converted to glucose),

ketogenic (potentially be converted to ketone bodies) and both glucogenic and ketogenic.

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Muhammad Wajid
Assistant Professor of Pharmaceutical Chemistry, Gulab Devi Institute of Pharmacy, Lahore
 Glucogenic Amino Acids:

Those amino acids in which their carbon skeleton gets degraded to pyrurate, α ketoglutarate,
succinyl CoA, fumrate and oxaloacetate and then converted to Glucose and Glycogen, are
called as Glucogenic amino acids. These include: alanine, aspartate, glycine, methionine etc.

Ketogenic amino acids:

Those amino acids, in which their carbon skeleton is degraded to Acetoacetyl CoA, or acetyl
CoA then converted to acetone and β-hydroxy butyrate which are the main ketone bodies are
called ketogenic amino acids. Leucine and lysine are exclusively ketogenic.

These amino acids have ability to form ketone bodies which is particularly evident in
untreated Diabetes mellitus in which large amounts of ketone bodies are produced by the
liver (i.e. not only from fatty acids but also from ketogenic amino acids). Degradation of
Leucine which is an exclusively ketogenic amino acid makes a substantial contribution to
ketone bodies during starvation.

Ketogenic and glucogenic Amino Acids:

The division between ketogenic and glucogenic amino acids is not sharp for amino acids
(Tryptophan, phenylalanine, tyrosine and Isoleucine are both ketogenic and glucogenic).
Some of the amino acids that can be converted in to pyruvate, particularly (Alanine, Cysteine
and serine, can also potentially form acetoacetate via acetyl CoA especially in severe
starvation and untreated diabetes mellitus.

Classification of amino acids based on polarity:

Amino acids are classified into 4 groups based on their polarity.

Non-polar amino acids:

These amino acids are also referred to as hydrophobic (water hating). They have no charge on
the 'R' group.

Polar amino acids with no charge on 'R' group:

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Muhammad Wajid
Assistant Professor of Pharmaceutical Chemistry, Gulab Devi Institute of Pharmacy, Lahore
These amino acids, as such, carry no charge on the 'R' group. They however
possess groups such as hydroxyl, sulfhydryl and amide and participate in hydrogen bonding
of protein structure. The simple amino acid glycine (where R = H) is also considered in this
category.

Polar amino acids with positive 'R' group:

The three amino acids lysine, arginine and histidine are included in this group.

Polar amino acids with negative 'R' group:

The dicarboxylic monoamino acids aspartic acid and glutamic acid are considered in this
group.

Properties of Amino acids:

Physical Properties:

They are colourless, crystalline substances, more soluble in water than in polar solvents.
Tyrosine is soluble in hot water. They have high melting point usually more than 200°C.
They have a high dielectric constant. They possess a large dipole moment.

Isomerism:

Two types of isomerism are shown by amino acids basically due to the presence of
asymmetric carbon atom. Glycine has no asymmetric carbon atom in its structure hence is
optically inactive.

Stereoisomerism:

All amino acids except glycine exist in D and L isomers. In D-amino acids –NH2 group is on
the right hand while in L-amino acids it is oriented to the left. It is the same orientation of OH
group of the central carbon of glyceraldehyde. Natural proteins of animals and plants
generally contain L-amino acids. D-amino acids occur in bacteria.

COOH COOH

H C NH2 H2N C H

R R

D-amino acid L-Amino acid 12

Muhammad Wajid
Assistant Professor of Pharmaceutical Chemistry, Gulab Devi Institute of Pharmacy, Lahore
 Optical Isomerism:

All amino acids except glycine have asymmetric carbon atom. Few amino acids like
isoleucine and threonine have an additional asymmetric carbon in their structures.
Consequently all but glycine exhibit „optical‟ activities and rotate the plane of plane polarised
light and exist as dextrorotatory (d) or laevorotatory (l) isomers. Optical activity depends on
the pH and side chain.

Amphoteric properties:

Amino acids due to the presence of their ionizable α –amino and α- carboxylic groups can act
as sometimes as acids and sometimes as bases depending on the pH of the media. This
property is called as amphoteric and therefore amino acids are called as ampholytes.

Chemical Properties of amino acids:

Amino acids show different types of chemical reactions. These reactions are due to different
groups attached to amino acids. These reactions are due to:

o Reactions due to amino group

o Reactions due to carboxyl group
o Reactions due to side chain
o Reaction due to both amino and carboxyl groups
Reactions due to amino group:
Reactions with Acids:

The amino groups behave as bases and combine with acids (e.g. HCl) to form salts (NH3Cl-).

NH2 NH3Cl

H C COOH HCl H C COOH

NH2 H

Glycine Hydrochloric acid Glycine Hydrochloride

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Muhammad Wajid
Assistant Professor of Pharmaceutical Chemistry, Gulab Devi Institute of Pharmacy, Lahore
 Reaction with formaldehyde:

Formaldehyde reacts with the -NH2 group to form a methylene compound.

CH2
NH2 N

R C COOH HCHO R C COOH

H H
Formaldehyde

Reaction with HNO2:

Like other primary amines, the amino acids except proline and hydroxyproline react with
HNO2 (nitrous acid) liberating N2 from NH2 group.

NH2 OH

R C COOH NHO2
R C COOH N2 H2O

H H
Nitric Acid
-Hydroxy Acid

Oxidation:

Potassium permanganate or H2O2 oxidises the NH2 group and converts the amino acid into
imino acid which reacts with water to form NH3 and α-keto acid.

NH2
H2 H2
HOOC C C C COOH H2O

Glutamic acid
O
H2 H2
HOOC C C C COOH NH3

-Ketoglutarate

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Muhammad Wajid
Assistant Professor of Pharmaceutical Chemistry, Gulab Devi Institute of Pharmacy, Lahore
 Transamination:

Transfer of an amino group from an amino acid to a keto acid to form a new amino acid is
called as transamination.

NH3 O O NH2
H C COOH C COO C COO HC COO
R1 R2 R1 R2

Amino Acids keto Acid Keto acid Amino acid

Reaction with CO2:

The amino acid anion present in an alkaline solution may react with CO2 through NH2
group to form a carbamino acid anion.

H H

Protein CO2 Protein RN

NH
COOH
Carbamino group

Reactions due to carboxyl group:

Formation of esters:

They can form esters with alcohols. The COOH group can be esterified with alcohol.

COOH COOR

R C H R-OH R C H H2O

NH2 NH2

Amino acid Alcohol

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Muhammad Wajid
Assistant Professor of Pharmaceutical Chemistry, Gulab Devi Institute of Pharmacy, Lahore
 Decarboxylation:

Amino acids undergo decarboxylation to produce corresponding amines.

COOH
H
R C H R C H CO2

NH2 NH2

Amino acid

Reaction with ammonia:

The carboxyl group of dicarboxylic amino acids reacts with NH3 to form amide.

Asparatic acid NH3 Asparagine

NH3 Glutamine
Glutamic acid

Salt formation:

Amino acids form salts (-COONa) with base NaOH.

COOH H2O NaOOC

R C NH2 NaOH R C NH2

H H

Amino Acid Base

Sodium salt of amino acid

Reaction due to side chain:

Formation of disulphide bond:

Cysteine has a sulfhydryl group (SH) group and can form a disulphide (S-S) bond with
another cysteine residue. Two cysteine residues can connect two polypeptide chains by the
formation of inter chain disulphide chains.

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Muhammad Wajid
Assistant Professor of Pharmaceutical Chemistry, Gulab Devi Institute of Pharmacy, Lahore
 O
O
H2N CH C OH
H2N CH C OH
CH2
CH2
Cysteine
SH2
S

SH Cystine
S

Cysteine CH2
CH2

HO C CH NH2
HO C CH NH2

O
O

Reaction due to both amino and carboxyl groups:

Formation of peptide bond

R R

HOOC C NH2 HOOC C NH2

H H

R O R
H
HOOC C N C C NH2

H H

Dipeptide Bond

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Muhammad Wajid
Assistant Professor of Pharmaceutical Chemistry, Gulab Devi Institute of Pharmacy, Lahore
 Physico-chemical classification:

These include simple proteins, compound proteins and derived proteins

Simple protein:

These are further sub classified based on their solubilities and heat coagulabilities. These
properties depend on the size and shape of the protein molecule. Major subclasses of simple
proteins are as follows:

o Albumin
o Globulin
o Globin
o Prolamine
o Histone
o Protamine
o Albuminoids
o Keratin
o Collagen
o Elastin
Albumin:

It is synthesized only in the liver. It is water soluble. It coagulates by the heat. It has carrier
function in the blood e.g. it carries Ca+2, bile salts, bilirubin, fatty acids, steroids etc. It exerts
oncotic pressure in the plasma. Its deficiency results in the loss of carrier functions, and
decreased oncotic pressure, which causes oedema etc.

Globulin:

It is synthesized in liver and spleen. It is water insoluble. Its β fraction has its carrier function
like transferrin. Its gamma fraction has defensive function like gamma globulin. There are
five classes of antibodies.

o IgM
o IgG
o IgA

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Muhammad Wajid
Assistant Professor of Pharmaceutical Chemistry, Gulab Devi Institute of Pharmacy, Lahore
 o IgD
o IgE
Globin:

It is the part of the hemoglobin. Normal adult hemoglobin is composed of four globin chains
i.e. two identical α chain and two identical β chains. Deficiency of any of the globin chains in
hemoglobin results in thalassemia. Mutation of the β globin chain at carbon no.6 where
glutamic acid is replaced by valine, results in sickle cell anemia.

Histones:

These are basic proteins, rich in arginine and histidine, with alkaline isoelectric pH. They do
not readily coagulate on heating. It combines with nucleic acid (DNA and RNA) to form
nucleoprotein (nucleo-histones). Examples: Nucleohistones, chromosomal nucleoproteins and
globin of haemoglobin.

Prolamine:

Alcohol soluble plant proteins, insoluble in water or salt solutions and absolute alcohol, but
they dissolve in 50 to 80 per cent ethanol. They are very rich in proline, but poor in lysine.
Examples: Gliadin of wheat and hordein of barley.

Protamine:

These are small molecules and are soluble in water, dilute acids and alkalies and dilute
ammonia and noncoagulable by heat. They do not contain cysteine, tryptophan and tyrosine
but are rich in arginine. They are basic proteins because they are rich in arginine (basic
Amino Acids). It combines with nucleic acids to form nucleoproteins. Examples are salmine,
sardinine and cyprinine of fish (sperms) and testes.

Albuminoids or Scleroproteins:

These are fibrous proteins with great stability and very low solubility and form supporting
structures of animals. Albuminoids are of three types:

o Keratin
o Collagen
o Elastin

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Muhammad Wajid
Assistant Professor of Pharmaceutical Chemistry, Gulab Devi Institute of Pharmacy, Lahore
 Conjugated or Compound proteins:

Conjugated proteins are simple proteins combined with a non-protein group called prosthetic
group. Protein part is called apoprotein, and entire molecule is called holoprotein. These
include the following types:

Nucleoprotein:

The nucleoproteins are compounds made up of simple basic proteins such as protamine or
histone with Nucleic Acids as the prosthetic group. They are proteins of cell nuclei and
apparently are the chief constituents of chromatin. They are most abundant in tissues having
large proportion of nuclear material such as yeast, asparagus tips in plants, thymus, other
glandular organs and sperm e.g. DNA and RNA.

Phosphoproteins:

These are the proteins with phosphoric acid as organic phosphate but not the phosphate
containing substances such as nucleic acids and phospholipids. (a) Casein and (b) Ovovitellin
are the two important groups of phosphoproteins found in milk, egg-yolk respectively.

Lipoprotein:

The lipoproteins are formed in combination with lipids as their prosthetic group.

Glycoprotein:

Mucoproteins are the simple proteins combined with mucopolysaccharides (MPS) such as
hyaluronic acid and the chondroitin sulphate. For example: Hyaluronic acids, Chondroitin
sulfate.

Chromoprotein:

These are proteins that contain coloured substance as the prosthetic group For example:
Hemoglobin, Cytochrome, and Rhodopsin.

Metallic Proteins:

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Muhammad Wajid
Assistant Professor of Pharmaceutical Chemistry, Gulab Devi Institute of Pharmacy, Lahore
As the name indicates, they contain a metal ion as their prosthetic group. Several enzymes
contain metallic elements such as Fe, Co, Mn, Zn, Cu, Mg, etc. Examples: Ferritin: Contains
Fe, Carbonic Anhydrase: Contains Zn, Ceruloplasmin: Contains Cu.

Derived Proteins:

These are derived from simple or compound proteins by denaturation or hydrolysis. They
include primary and secondary derived proteins.

Primary derived proteins:

Denatured or coagulated proteins are placed in this group. Their molecular weight is the same
as native protein, but they differ in solubility, precipitation and crystallisation. Heat, X-ray,
UV rays, vigorous shaking, acid, alkali cause denaturation and give rise to primary derived
proteins. There is an intramolecular rearrangement leading to changes in their properties such
as solubility. Primary derived proteins are synonymous with denatured proteins in which
peptide bonds remain intact.

Secondary derived proteins:

These are the proteins formed by the progressive hydrolysis of proteins at their peptide
linkages. They represent a great complexity with respect to their size and amino acid
composition. They are roughly called as proteoses, peptones and peptides according to
relative average molecular size.

Structural organization of proteins:

Protein structure is normally described at four levels of organisation.

o Primary Structure
o Secondary Structure
 Super Secondary Structure
o Tertiary Structure
o Quaternary Structure
Primary Structure:

Primary structure is the linear sequence of amino acids held together by peptide bonds in its
peptide chain. The peptide bonds form the backbone and side chains of amino acid residues
project outside the peptide backbone. The free -NH2 group of the terminal amino acid is
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Muhammad Wajid
Assistant Professor of Pharmaceutical Chemistry, Gulab Devi Institute of Pharmacy, Lahore
called as N-terminal end and the free -COOH end is called as C-terminal end. It is a tradition
to number the amino acids from N-terminal end as No. 1 towards the C-terminal end. Amino
acids in peptides and proteins are joined together by peptide bonds (amide Bond). The
backbone of all proteins consists of N-C-C repetitive unit. Only the R-group side-chains vary.

R
H H O R H
O O
R R R
N C N C
C N C OH
C
H C N C C N C C
H H

H H O H H O H

Each amino acid is called residue. The polypeptide chain consists of repeating units that
make up the backbone. The variable portion of the polypeptide chain is the side chain. The
peptide chain has ability to form hydrogen bonding

o Hydrogen bond donor: N-H group

o Hydrogen bond acceptor: C=O group

Polypeptide chain shows double bond character

R
H R
H H
C N H
C C
C N
H C C
R H
O
O- R

In majority of the cases, trans-peptide bonds are energetically more favorable than Cis
because there is no bumping of atoms.

HN
C
C

H R
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Muhammad Wajid
Assistant Professor of Pharmaceutical Chemistry, Gulab Devi Institute of Pharmacy, Lahore
φ= is angle of rotation about the single bond between the nitrogen and α- carbon

ψ = angle of rotation about the single bond between α- carbon and the carboxyl carbon atom

The φ and ψ rotations ultimately allow the protein to ultimately folds into three dimensional
structures. Note that not all the φ and ψ rotations are possible due to stearic hindrance.

Secondary Structure:

The peptide chain thus formed assumes a three dimensional secondary structure by way of
folding or coiling consisting of a helically-coiled, zigzags, linear or mixed form. It results
from the steric relationship between amino acids located relatively near each other in the
peptide chain. The linkages or bonds involved in the secondary structure formation are
hydrogen bonds and disulfide bonds.

Hydrogen bond:

These are weak, low energy non covalent bonds sharing single hydrogen by two
electronegative atoms such as O and N. Hydrogen bonds are formed in secondary structure
by sharing H-atoms between oxygen of CO and nitrogen of -NH of different peptide bonds.
The hydrogen bonds in secondary structure may form either α-helix or β-pleated sheet
structure.

Disulphide bonds:

These are formed between two cysteine residues. They are strong, high energy covalent
bonds.

α-Helix:

A peptide chain forms regular helical coils called α--helix. These coils are stabilized by
hydrogen bonds between carbonyl O of 1st amino and amide N of 4th amino acid residues.
Thus in α--helix intra chain hydrogen bonding is present. The α--helices can be either right
handed or left handed. Left handed α--helix is less stable than right handed α--helix because
of the steric interference between the C = O and the side chains. Only the right handed α--
helix has been found in protein structure.

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Muhammad Wajid
Assistant Professor of Pharmaceutical Chemistry, Gulab Devi Institute of Pharmacy, Lahore
 Triple helix:

Type-2 helix or triple helix is a major shape in secondary structure. It consists of a triple helix
made of the repetitious amino acid sequence glycine- proline – hydroxyproline.

β pleated sheet:

Two main forms of  pleated sheets

o Antiparallel  pleated sheet

o Parallel  pleated sheet

Antiparallel  pleated sheet in which the neighboring hydrogen bonded polypeptide chains
run in opposite directions.

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Muhammad Wajid
Assistant Professor of Pharmaceutical Chemistry, Gulab Devi Institute of Pharmacy, Lahore
Parallel  pleated sheet in which the hydrogen bonded chains extend in the same direction.

O R H O
O H
H R R
H N C OH
R N C C
N C C
C C C
N C N
C H R H
H H H O H
O H
O R H O R H O

H2 H R
C N C CH N C CH N C OH
C C N C C C
H2N N C
H2
H
O H O R O
H H

Sheets can be made up of any number of strands. Orientation and hydrogen bonding pattern
of strands gives rise to flat or twisted sheets. Parallel sheets buried inside, while antiparallel
sheets occurs on the surface.

Reverse Turns or β-bends:

Since the polypeptide chain of a globular protein changes direction two or more times when it
folds, the conformations known as reverse turns or β-bends are important elements of
secondary structure. Reverse turns usually occur on the surfaces of globular proteins where
there is little steric hindrance to resist a change in the direction of the polypeptide chain.

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Muhammad Wajid
Assistant Professor of Pharmaceutical Chemistry, Gulab Devi Institute of Pharmacy, Lahore
 Super Secondary Structure:

Secondary structures often group together to form a specific geometric arrangements known
as motifs. Since motifs contain more than one secondary structural element, these are referred
to as super secondary structures. Simple motifs can combine to form more complex motifs.
These are:

o β-α-β unit
o Greek Key
o β-meander
β-α-β Unit:

The β-α-β Unit consists of two parallel β- pleated sheets connected by an intervening strand
of α- helix.

Greek key:

The Greek key motif consists of four adjacent antiparallel strands and their linking loops. It
consists of three antiparallel strands connected by hairpins, while the fourth is adjacent to the
first and linked to the third by a longer loop.

β-meander:

The β -meander consists of five β –pleated sheets connected by reverse turns. The β -meander
contains nearly as many hydrogen bonds as an α-helix, and its common occurrence probably
reflects the stability conferred by this extensive hydrogen bonding.

26
Muhammad Wajid
Assistant Professor of Pharmaceutical Chemistry, Gulab Devi Institute of Pharmacy, Lahore
 Tertiary structure

The three-dimensional arrangement of protein structure is referred to as tertiary structure. It is

a compact structure with hydrophobic side chains held interior while the hydrophilic groups
are on the surface of the protein molecule. This type of arrangement ensures stability of the
molecule.

Bonds of tertiary structure:

Besides the hydrogen bonds, disulfide bonds (-S-S), ionic interactions (electrostatic bonds)
and hydrophobic interactions also contribute to the tertiary structure of protein.

Quaternary Structure:

A great majority of the proteins are composed of single polypeptide chains. Some of the
proteins, however, consist of two or more polypeptides which may be identical or
"unrelated. Such proteins are termed as oligomers and possess quaternary structure. The
individual polypeptide chains are known as monomers, protomers or subunits. A dimer
consists of two polypeptides while a tetramer has four.

Bonds in quaternary structure:

The monomeric subunits are held together by non-covalent bonds namely hydrogen bonds,
hydrophobic interactions and ionic bonds.

Biological Application of Proteins:

o All Enzymes are proteins in nature so they control whole metabolism process
o Proteins build many Structures of the cell (e.g keratin which makes nail and hair)
o Proteins are the major component of cell membrane about 60 – 80%
o Some proteins works as carriers which transport specific substances such as
o oxygen
o lipids
o metal ions (e.g. Hemoglobin)
o Some of the proteins called Antibodies which defend the body against pathogens
o Help in the coagulation of blood e.g. fibrinogen and prothrombin
o Provide defense to the body e.g. γ-globulins (immunoglobulins) produce antibodies
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Muhammad Wajid
Assistant Professor of Pharmaceutical Chemistry, Gulab Devi Institute of Pharmacy, Lahore
 o Help in muscle contraction e.g. actin and myosin

Pharmaceutical Application of Protein:

More than 200 pharmaceutical proteins which have been investigated so for. More than half
are undergoing research and development. About 100 are in clinical trials and a dozen or so
have already been marketed. Hormones are also proteins which are used pharmaceutically.

Insulin:

Insulin is a protein comprising of 2 polypeptide chains A (with 21 amino acid residues) and B
(with 30 amino acid residues). Chains A and B are linked by disulphide bridges. A-chain
contains an intra-chain disulphide bridge linking residue 6 and 11. Insulin is used for the
treatment of diabetes mellitus.

Types of insulin:

Insulin analogues which are synthetically modified with some changes in the amino acid
sequence are also available. These are:

o Insulin Lispro
o Insulin Aspart
o Insulin Glulisine
o Insulin Glargine
o Insulin Detemir
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Muhammad Wajid
Assistant Professor of Pharmaceutical Chemistry, Gulab Devi Institute of Pharmacy, Lahore
 Vasopressin:

The vasopressin is peptides consisting of nine amino acids (nonapeptides). Vasopressin is

used to manage anti-diuretic hormone deficiency.

Oxytocin:

Oxytocin is a peptide of nine amino acids (a nonapeptide). Oxytocin is used to induce labor
or strengthen labor contractions during childbirth, and to control bleeding after childbirth.
Oxytocin is also used to stimulate uterine contractions in a woman with an incomplete or
threatened miscarriage.

Chelated protein:

A chelate is a chemical compound in which a metal molecule (mineral) and an organic

molecule (ligand) for example protein are combined. For example Iron chelated protein is an
iron supplement used to treat or prevent low blood levels of iron (e.g., for anemia or during
pregnancy).

Peptide antibiotics:

Antibiotics such as:

o Gramicidin
o Bacitracin
o Tyrocidin
o Actinomycin

These are peptide in nature.

29
Muhammad Wajid
Assistant Professor of Pharmaceutical Chemistry, Gulab Devi Institute of Pharmacy, Lahore