PROTEINS

Proteins are polymers of amino acids linked together by peptide

bonds. Molecular structures consisting of 2 to 100 amino acids with
molecular weight up to 10 kDa are usually called peptides. Longer
polypeptide structures are classified as proteins.

Peptides have many different conformations and can randomly

change them, whereas proteins are structurally more rigid with only
one preferable conformation.

It is almost impossible to estimate the total number of different

proteins in nature. For example only in E. coli cell, about 3000
different proteins are known.
CLASSIFICATION OF PROTEINS BASED ON FUNCTION

Enzymes Hormones

Transport Proteins Protective Proteins

Structural Proteins Motor Proteins

Receptors Signaling Proteins

Storage Proteins
ENZYMES

These proteins catalyze chemical and biochemical reactions within living cell and
outside.

This group of proteins probably is the biggest and most important group of the proteins.

Enzymes are responsible for all metabolic reactions in the living cells.

Well known and very interesting examples are: DNA/ RNA polymerases,
dehydrogenases etc.
HORMONES

These proteins are responsible for the regulation of many

processes in organisms.

Protein hormones are usually quite small and can be

classified as peptides.

Most known protein hormones are: insulin, some growth

factors, lipotropin, prolactin, enkephalin etc
TRANSPORT PROTEINS

These proteins are transporting or storing some other chemical compounds and ions.

Some of common examples are cytochrome C in the electron transport; hemoglobin

and myoglobin in oxygen transport; albumin in fatty acid transport in the blood stream
etc.

It is also possible to classify trans-membrane protein channels as a transport proteins

as well.
PROTECTIVE PROTEINS

These proteins are involved in the immune response of the organism to neutralize large
foreign molecules, that can be a part of an infection.

This group of proteins consists of protective proteins such as lymphocyte antigen-

recognizing receptors, antiviral agents, interferon, tumor necrosis factor (TNF) etc

Probably the proteins responsible for blood clotting such as fibrin and thrombin should
be classified as protective proteins as well.
STRUCTURAL PROTEINS

These proteins maintain the structures of other biological components,

like cells and tissues.

Some common examples of these proteins are collagen, elastin, α-

keratin, and fibroin.

Bacterial proteoglycans and viral coating proteins also belongs to this

group of proteins.
MOTOR PROTEINS

These proteins can convert chemical energy into mechanical

energy.

Some common examples of these proteins are actin and myosin.

These proteins are responsible for muscular motion.
RECEPTOR PROTEINS

These proteins are responsible for signal detection and translation of these signals.

Sometimes these proteins are active only in complex with low molecular weight
compounds. A very well known member of this protein family is rhodopsin, a light
detecting protein present in the eye.

Many receptor proteins are also found in the surfaces of cell membranes.
STORAGE PROTEINS

These proteins contain energy, which can be released during metabolic

processes in the organism.

Some common examples of storage proteins are ovalbumin-water soluble

protein present in egg white, and casein-proteins found in milk.

Almost all proteins can be digested and used as a source of energy and
building material by other organisms.
CLASSIFICATION OF PROTEINS BASED ON SOLUBILITY

Albumins

Globulins

Glutelins

Prolamines

Protamines

Histones
ALBUMINS

Albumins are globular proteins that are soluble in water and dilute salt solution.

They are precipitated by saturating the protein solution with ammonium sulfate. They
are also coagulated by heat.

These proteins are found in both plant and animal tissues. Examples of these proteins
are serum albumin in the blood; milk albumin; egg white albumin; legumelin; phaseolin
etc
GLOBULINS

Globular protein are sparingly soluble in water but soluble in dilute

neutral salt solutions.

They are precipitated by dilute ammonium sulfate solution and

coagulated by heat.

Globulins are distributed in both plant and animal tissues. Some

common examples are blood serum globulins; muscle proteins
(myosin); potato proteins (tuberin); Brazil nut proteins (excelsin);
hemp proteins (edestin); lentil proteins (legumin) etc.
GLUTELINS

These proteins are insoluble in water and dilute salt solutions.

However, they are soluble in dilute acid solutions.

These proteins are found in grains and cereals. Some common

examples are wheat proteins (glutenin); and rice protein
(oryzenin).
PROLAMINES

These proteins are insoluble in water and absolute alcohol.

However, they are soluble in 70% alcohol;

These proteins are high in amide nitrogen and proline.

They occurs in grain seeds. Some common examples are wheat

and rye proteins (gliadin); corn protein (zein); rye protein (secaline);
and barley protein (hordein).
PROTAMINES

These proteins are soluble in water. However, they are not coagulated by heat.

They are strongly basic due to a high arginine content. They are found associated with
DNA material.

They occurs in sperm cells. Some common examples are sturgeon protein (sturine);
mackerel protein (scombrine); salmon protein (salmine) etc.
HISTONES

These proteins are soluble in water, salt solutions, and dilute acids.
However, they are insoluble in ammonium hydroxide and yields large
amounts of lysine and arginine upon hydrolysis.

They also found combined with nucleic acids within cells. A common
example is the nucleohistone found in the thymus gland and
pancreas.
STRUCTURAL PROTEINS
Collagen
These proteins form the connective tissues, bones, cartilage, and gelatin. They are resistant
to digestive enzymes but are digested by boiling water, acid solution, or alkali solution. They
also contain high amounts of hydroxyproline

Elastin
These proteins form the ligaments, tendons, and arteries. They are similar to collagen but
cannot be converted to gelatin.

Keratin
These proteins from the hair, nails, hooves, horns, and feathers of animals. They are partially
resistant to digestive enzymes; contains large amounts of sulfur amino acids like cysteine.
CONJUGATED PROTEINS

Nucleoproteins
These proteins contain nucleic acids, nitrogen, and phosphorus. They are often found in
chromosomes or combined with either RNA or DNA.

Some common examples are ribonucleoprotein, deoxyribonucleoprotein, and the proteins

found in viruses, and bacteriophages.

Mucoprotein
These proteins combined with amino sugars, sugar acids, and sulfates. Some common
examples are mucin in saliva; and egg white protein called ovomucoid
CONJUGATED PROTEINS

Glycoprotein
These proteins contain more than 4% hexosamine. They are the glycoproteins found
in the bone (osseomucoid); in the tendons (tendomucoid); and in the carilage
(chondromucoid).

Phosphoproteins
These proteins contain phosphoric acid joined in ester linkages to a protein molecule.
Some common examples of these proteins are milk proteins (casein) and egg yolk
protein (ovovitellin).
CONJUGATED PROTEINS
Chromoproteins
These proteins contain nonprotein pigments as heme. Some common examples are
hemoglobin, myoglobin, flavoproteins, respiratory pigments and cytochromes.

Lipoproteins
These are water-soluble protein conjugated with lipids. They are commonly found dispersed
widely in cells as serum lipoprotein; in brain, nerve tissues, milk, and eggs.

Metalloproteins
These are proteins are combined with metallic atoms that are not parts of a non-protein
prosthetic group. Some common examples are ferritin, carbonic anhydrase, and ceruloplasmin.
DERIVED PROTEINS

Proteans
These proteins are products of the action of acids or enzymes on other proteins. These
proteins are insoluble in water. Some common examples are edestan (from elastin) and
myosan (from myosin).

Proteases
These proteins are soluble in water; uncoagulated by heat; and precipitated by saturated
ammonium sulfate. They are a result of the partial digestion of protein by pepsin or trypsin.
DERIVED PROTEINS

Peptones
These proteins are intermediate products of protein digestion. They have the same
properties as proteases except that they cannot be salted out due to their small
molecular weight.

Peptides
They are intermediate products of protein digestion. Usually, they consists of two or
more amino acids joined by a peptide linkage.
PROTEIN STRUCTURE
PROTEIN STRUCTURE

Primary Structure

The primary structure refers to the amino acid sequence in the

polypeptide chain or protein. It serves as the basis for the other
higher order structure in proteins.

The dominant chemical bond used in the primary structure is

covalent bond.
PROTEIN STRUCTURE

Secondary Structure

Secondary structure refer to local folding/ structural motif in the

polypeptide chain. The three (3) types of secondary structures are:

-α helical structure

-β pleated sheets

- random coil
PROTEIN STRUCTURE

Secondary Structure

One of the main conformational parameter of the amino acid structure is the value of the phi
and psi angles. These angles completely define the conformation of the polypeptide chain.

With some special values for these angles the main chain can adopt specially classified
conformations, like alpha-helix or beta-strand.

The other main feature of the protein secondary structure is the local stabilisation by
hydrogen bonds.
PROTEIN STRUCTURE
Secondary Structure
PROTEIN STRUCTURE

Secondary Structure
PROTEIN STRUCTURE

Some amino acids like methionine, alanine, leucine, and lysine makes the protein more likely
to form a α-helical structure. They are usually found in keratins of hair, feathers and nails.

On the other hand, amino acids like tyrosine, phenylalanine, tryptophan, valine and isoleucine
makes the protein more likely to form a β-pleated sheet structure. Polypeptides with beta-
pleated sheet structures usually form soft flexible filaments such as the silk fibroin.
PROTEIN STRUCTURE

If the polypeptide chain has many glutamic acid residues, this segment will not form α-helical structure.
Also, presence of many lys/ arg at pH 7.0 will prevent formation of α-helical structure.

Asn, Ser, Thr, and leu residues also tend to prevent formation of α-helical structure.

The presence of proline also inhibits α-helical structure. Positively charged amino acids at the N-
terminal and negatively charged amino acids at the C terminal are destabilizing to α-helical structure.
PROTEIN STRUCTURE

The Ramachandran plot tells us whether the protein will have α-helical
structure or β-pleated sheet structure.

This depends on the value of Ψ and Φ.These are the two torsion angles
present in polypeptide chains. Torsion angles are among the most important
local structural parameters that control protein folding.
PROTEIN STRUCTURE
PROTEIN STRUCTURE
PROTEIN STRUCTURE

Ternary Structure
The ternary structure of the protein completely define the structural organization of
the protein molecule in 3d.

Quaternary Structure
The quaternary structure results from the interaction between several protein
molecules to form protein complexes. These structure are held together by strong
covalent bond such as disulfide linkages.