Proteins

• A protein is a naturally occurring,

unbranched polymer in which the
monomer units are amino acids. Thus
the starting point for a discussion of
proteins is an understanding of the
structures and chemical properties of
amino acids.

• Next to water, proteins are the most

abundant substances in nearly all cells-
they account for about 15 % of a cells
overall mass and for almost half of a
cells dry mass.

• All proteins contain the elements

carbon, hydrogen, oxygen, and Amino Acids-Properties, Structure,
nitrogen; most also contain sulfur. Classification and Functions

Structure of Proteins • Properties of Amino Acids

• Amino acids constitute a group of

neutral products clearly distinguished
from other natural compounds
chemically, mainly because of their
ampholytic properties, and
biochemically, mainly because of their
role as protein constituents.

• An amino acid is a carboxylic acid-

Figure 1: The relationship between amino acid
side chains and protein conformation
The defining feature of an amino acid is its side
chain (at top, blue circle; below, all colored
circles). When connected by a series of peptide
bonds, amino acids form a polypeptide, another
word for protein. The polypeptide will then fold
into a specific conformation depending on the
interactions (dashed lines) between its amino
acid side chains.
containing an aliphatic primary amino
group in the α position to the carboxyl
group and with a characteristic
stereochemistry.
• Proteins are biosynthesized from 20
amino acids in a system involving strict
genetic control. Thus, amino acids are
the basic unit of proteins.
• More than 300 amino acids are found in
nature but only 20 amino acids are
standard and present in protein
because they are coded by genes. Other
amino acids are modified amino acids
and called non-protein amino acids.
Physical Properties of Amino Acids
• Amino acids are colorless, crystalline
solid.
• All amino acids have a high melting
point greater than 200 ⁰C.
• Solubility: They are soluble in water,
slightly soluble in alcohol and dissolve
with difficulty in methanol, ethanol, and
propanol. R-group of amino acids and
pH of the solvent play important role in
solubility.
• On heating to high temperatures, they
decompose.
• All amino acids (except glycine) are
optically active.
• Peptide bond formation: Amino acids
can connect with a peptide bond
involving their amino and carboxylate
groups. A covalent bond formed
between the alpha-amino group of one
amino acid and an alpha-carboxyl group
of other forming -CO-NH-linkage.
Peptide bonds are planar and partially
ionic.
Chemical Properties
• 1.Zwitterionic property
• A zwitterion is a molecule with
functional groups, of which at least one
has a positive and one has a negative
electrical charge. The net charge of the
entire molecule is zero. Amino acids are
the best-known examples of
zwitterions. They contain an amine
group (basic) and a carboxylic group
(acidic). The -NH2 group is the stronger
base, and so it picks up H+ from the -
COOH group to leave a zwitterion. The
(neutral) zwitterion is the usual form
amino acids exist in solution.
• 2. Amphoteric property
• Amino acids are amphoteric in nature
that is they act as both acids and base
since due to the two amine and
carboxylic group present.
• 3. Ninhydrin test
• When 1 ml of Ninhydrin solution is
added to a 1 ml protein solution and
heated, the formation of a violet color
indicates the presence of α-amino acids.
• 4. Xanthoproteic test
• The xanthoproteic test is performed for
the detection of aromatic amino acids
(tyrosine, tryptophan, and
phenylalanine) in a protein solution.
The nitration of benzoid radicals present
in the amino acid chain occurs due to
reaction with nitric acid, giving the
solution yellow coloration. Reaction
with Sanger’s reagent
• 5. Reaction with Sanger’s Reagent
• Sanger’s reagent (1-fluoro-2, 4-
dinitrobenzene) reacts with a free
amino group in the peptide chain in a
mild alkaline medium under cold
conditions.
• 6. Reaction with nitrous acid
• Nitrous acid reacts with the amino
group to liberate nitrogen and form the
corresponding hydroxyl. All 20 of the
common amino acids are alpha-amino
acids. They contain a carboxyl group, an
amino group, and a side chain (R
group), all attached to the α-carbon.

• Exceptions are:
• Glycine, which does not have a side
chain. Its α-carbon contains two
hydrogens.
• Proline, in which nitrogen is part of a
ring.
• Thus, each amino acid has an amine
group at one end and an acid group at
the other and a distinctive side chain.
The backbone is the same for all amino
acids while the side chain differs from
one amino acid to the next.
• All of the 20 amino acids except glycine
are of the L-configuration, as for all but
one amino acid the α-carbon is an
asymmetric carbon. Because glycine
does not contain an asymmetric carbon
atom, it is not optically active and, thus,
it is neither D nor L.
Classification of amino acids on the basis of the
R group
• Nonpolar, Aliphatic amino acids: The R
groups in this class of amino acids are
nonpolar and hydrophobic. Glycine,
Alanine, Valine, leucine, Isoleucine,
Methionine, Proline.
• Aromatic amino acids: Phenylalanine,
tyrosine, and tryptophan, with their
aromatic side chains, are relatively
nonpolar (hydrophobic). All can
participate in hydrophobic interactions.
• Polar, Uncharged amino acids: The R
groups of these amino acids are more
soluble in water, or more hydrophilic,
than those of the nonpolar amino acids,
because they contain functional groups
that form hydrogen bonds with water.
This class of amino acids includes
serine, threonine, cysteine, asparagine,
and glutamine.
• Acidic amino acids: Amino acids in
which R-group is acidic or negatively
charged. Glutamic acid and Aspartic
acid
• Basic amino acids: Amino acids in which
R-group is basic or positively charged.
Lysine, Arginine, Histidine
Classification of Amino Acids on the basis of
Nutrition
• 1.Essential amino acids (9) is a standard
amino acid needed for protein synthesis
that must be obtained from dietary
 sources because the human body can
not synthesize in adequate amounts
from other substances.
• Nine amino acids cannot be synthesized
in the body and, therefore, must be
present in the diet in order for protein
synthesis to occur.
• These essential amino acids are
histidine, isoleucine, leucine, lysine,
methionine, phenylalanine, threonine,
tryptophan, and valine.
• Incomplete dietary protein is a protein
that does not contain adequate
amounts, relative to the body’s needs,
of one or more of the essential amino
acids. Associated with the term
incomplete dietary protein is the term
limiting amino acid. A limiting amino
acid is an essential amino acid that is
missing, or present in inadequate
amounts in an incomplete dietary
protein.

• 2. Non-essential amino acids (Eleven)

• These amino acids can be synthesized in

the body itself and hence not
necessarily need to be acquired through
diet.

• Arginine, glutamine, tyrosine, cysteine,

glycine, proline, serine, ornithine,
alanine, asparagine, and aspartate.

• 3. Conditionally

Classification of Amino Acids on the basis of

metabolic fate

CLASSIFICATION OF AMINO ACIDS ON

THE BASIS OF METABOLIC FATE

• 1. Glucogenic amino acids: These

Complete dietary Protein and Incomplete
Dietary Protein
• Complete dietary protein is a protein
that contains of all the essential amino
acids in the same relative amounts in
which the body needs them. It may or
may not contain all of the essential
amino acids.
amino acids serve as precursors
gluconeogenesis for glucose formation.
Glycine, alanine, serine, aspartic acid,
asparagine, glutamic acid, glutamine,
proline, valine, methionine, cysteine,
histidine, and arginine.
• 2. Ketogenic amino acids: These amino
acids breakdown to form ketone bodies.
Leucine and Lysine.
• 3. Both glucogenic and ketogenic
amino acids: These amino acids
breakdown to form precursors for both
ketone bodies and glucose. Isoleucine,
Phenylalanine, Tryptophan, and
tyrosine.
Functions of Amino Acids
• 1. In particular, 20 very important
amino acids are crucial for life as they
contain peptides and proteins and are
known to be the building blocks for all
living things.
• The nitrogen-containing substrates are
used in the biosynthesis of purines,
pyrimidines, neurotransmitters,
hormones, porphyrins, and
nonessential amino acids.
• The carbon skeletons are used as a fuel
source in the citric acid cycle, used for
gluconeogenesis, or used in fatty acid
synthesis.
Classification of Protein

• 2. The linear sequence of amino acid

residues in a polypeptide chain
determines the three-dimensional
configuration of a protein, and the
structure of a protein determines its
function.

• 3. Amino acids are imperative for

sustaining the health of the human
body. They largely promote the:

• Production of hormones

• Structure of muscles

• Human nervous system’s

healthy functioning

• The health of vital organs

Classification of Protein based on chemical
• Normal cellular structure composition
• The amino acids are used by various
tissues to synthesize proteins and to
produce nitrogen-containing
compounds (e.g., purines, heme,
creatine, epinephrine), or they are
oxidized to produce energy.

• The breakdown of both dietary and

tissue proteins yields nitrogen-
containing substrates and carbon
skeletons. This classification of protein is shape or
structure and composition. They are classified
into three types: fibrous, globular and derived
protein.
A. Fibrous protein:
• They are elongated or fiber like protein.
• Axial ratio (length: breadth ratio) is
more than 10
• They are static in nature with simple
structure.
• They have less biological functions
• They are mostly present in animals
• Fibrous proteins are further classified
as- simple and conjugated
• i. Simple fibrous protein:
• Examples; Scleroprotein (Keratine,
elastin, collagen, fibroin etc)
• Scleroprotein or Albuminoids: they
make animal skeleton and they are
water insoluble.
• Conjugated fibrous proteins:(pigments
present in chicken feather)
Globular Protein:
•They are spherical or globular in shape.
• Axial ratio is always less than 10
• They are dynamic in nature (can flow or
move) with higher degree of complexity
in structure.
• They have variety of biological functions
• Examples; enzymes, hormones etc
• Globular protein is further classified on
the basis of composition or solubility.
• They are composed of amino acids only.
• Some examples are;
• a. Protamine:
• They are positively charged (basic)
proteins mostly present in animals and
fishes (sperm)
• Protamines binds with DNA in
embryonic stage and later replaced by
histone
• It is soluble in water and ammonium
hydroxide solution
• It is not coagulated by heat
• It precipitate out in aqueous solution of
alcohol
• Protamine are rich in arginine and lysine
whereas devoid of sulfur containing and
aromatic amino acids.
• b. histone:
• They are basic protein but weak base in
comparison to protamine.
• Histone is low molecular weight protein
and are water soluble.
• It is not coagulated by heat.
• Histone is present in nucleic acids as
nucleohistone binding with DNA.
• c. Albumin:
• It is the most abundant protein in
nature
• It is most commonly found in seeds in
plants and in blood and muscles in
animals.
• Molecular weight of albumin is 65000
KD
• It is water soluble and can be
coagulated by heat
• Plant albumins; Leucosine, Legumelins
etc
• Animal albumins; serum albumin, • Eg. Ceruloplasmin; contains copper as
myosin, lactalbumin, ova-albumin etc. prosthetic group

• D. Globulin • Some other metals such as Calcium

weakly binds with protein. Eg.
• Pseudoglobulin (water soluble)and
Calsequestrin, calmodulin
Euglobulin (water insoluble)
• Some metals such as Na, K etc do not
• E. Glutelins
binds with protein but associate with
• A. Water insoluble. E.g. Gittenin nucleic acids protein.
(wheat)glutein(corn)oryzenin (rice)
• b. Chromoprotein:
• f. Prolamine:
• They have colored prosthetic group.
• They are storage protein found in seeds.
• Some examples are;
• They are water insoluble. But soluble in
• Haemoprotein: Haemoglobin,
dilute acid or detergents and 60-80%
myoglobin, chlorophyll, cytochrome,
alcohol.
peroxidase, haemocyanin
• They are coagulated by heat
• Flavoprotein: Riboflavin (Vit B2) give
• Prolamine is rich in proline and yellow/orange color to FAD requiring
glutamine enzymes

• Examples; Gliadin (wheat), zein (corn), • C. Glycoprotein/Muco Protein

Hordein (barley), Avenin (oats)
• They have carbohydrate as prosthetic
Complex or conjugate or hetero globular group
protein:
• Eg. Antibody, complement proteins,
• These proteins in which protein are Heparin, Hyaluronic acid
always linked by non-protein moiety to
• d. Phosphoprotein:
become functional. So, they are
composed of both protein and non- • They have phosphate group as
protein components. The non-protein prosthetic group.
component is known as prosthetic
• Eg. Caesein (milk protein binds with
group.
calcium ion to form calcium salt of
• On the basis of prosthetic group, they caseinate)
are classified as follows;
• Ovovitellin; present in egg yolk
• Metalloprotein:
• Calcineurin
• They have metal prosthetic group.
• Lipoprotein:
• Some metals such as Hg, Ag, CU, Zn etc,
• They have lipid as prosthetic group.
strongly binds with proteins such as
collagen, albumin, casein by –SH group • Eg. Lipovitelline, chylomicrons
of side chain of amino acids.
• Derived protein:
• These protein are the derivatives of
either simple or complex protein
resulting from the action of heat,
enzymes and chemicals.
• Some artificially produced protein are
included in this group.
• They are classified as primary derived
protein and secondary derived protein.
• Primary derived protein:
• The derived protein in which the size of
protein molecules are not altered
materially but only the arrangement is
changed.
• Some examples are;
• a. Proteans
• Obtained as a first product after the
action of acid or enzymes or water on
protein.
• They are insoluble in water.
• Eg. Edestan, myosin
• b. metaprotein
• They are produced by further action of
acid or alkali on protein at 30-60°C.
• They are water insoluble but soluble in
dil acid or alkali.
• Also known as Infraprotein.
• Eg. Curd
• Coagulated protein:
• They are produced by the action of heat
or alcohol on protein.
• They are insoluble in water.
• Eg. Coagulated egg
• Secondary derived protein:
• The derived protein in which size of
original protein are altered.
• Hydrolysis has occurred due to which
size of protein molecule are smaller
than original one.
• Examples; a) Proteoses:
• They are produced by the action of
dilute acid or digestive enzymes when
the hydrolysis proceeds beyond the
level of metaprotein.
• They are soluble in water
• They are not coagulated by heat. • Eg.
Albumose, Globulose etc.
Classification of proteins on the basis of
biological functions
• Catalytic proteins:
• They catalyze biochemical reaction in
cells Eg.enzymes and co-enzymes.
• Structural proteins:
• They make various structural
component of living being
• Ex.collagen make bone,Elastin make
ligaments and keratin make hair and
nails
• Nutrient Protein
• They have nutritional value and provide
nutrition when consumed.
• Regulatory proteins
• They have nutritional value and provide
nutrition when consumed.
• Ex. casein in milk.
• Defense Protein
• They provide defensive mechanism
against pathogens.
• Eg. Antibodies, complement proteins

• Transport Protein:

• They transport nutrients and other

molecules

• Ex.Haemoglabin

• Storage Protein:

• They store various molecules and ions

in cells.

• Ex.Ferritin store iron.

• Contractile/mobile protein:

• They help in movement and locomotion

of various body parts

• Ex.actin myosin,tubulin etc.

• Toxic protein:

• They are toxic and can damage tissues

• Eg.snake venom,bacterial exotoxins etc.

Summary of classification of proteins