Proteins

• Proteins are macromolecules having one or more polypeptides (chains of amino

acids). Thus proteins are the polymers of amino acids.
• They contain the elements carbon, hydrogen, oxygen and nitrogen and in some
cases sulphur.
• There are 20 different amino acids which are commonly found in naturally
occurring proteins.
• The variety of proteins is unlimited because the number and sequence of
arrangement of amino acids in each protein is specific and is genetically
controlled by DNA.
• Proteins are the most abundant organic molecules to be found in cells. They are
an essential component of the diet of animals and may be converted to both fats
and carbohydrate by the cells. They show a great range of structural and
metabolic activities within the cells.
 Types of bonds
• There are different types of
bonds that hold protein
molecule in shapes. They are
ionic bond, disulphide bond,
hydrogen bond and
hydrophobic interaction.
 Types of bonds
• Ionic bond: Bond formed between
ionized (charged) amine and carboxylic
groups (occurring in R group)of basic and
acidic amino acids respectively is called
as ionic bond.
• Acidic and basic R groups exist in
charged state at certain pH. Acidic R
groups are negatively charged and basic
R groups are positively charged. They can
therefore be attracted forming ionic
bonds.
• They are the strongest of all the
intramolecular bonds and can be broken
by change in pH.
 Types of bonds
• Disulphide bond: Bond formed between
sulphydryl (-SH) groups of two cysteine
molecules is called as disulphide bond.
• The amino acid cysteine contains a
sulphydryl group it is R group and if two
cysteine molecules line up alongside each
other, neighboring SH groups can be
oxidized (oxidation= removal of hydrogen)
forming disulphide bond.
• It may be formed between different
polypeptide chains or between different
parts of the same chain. In the later case
the disulphide bonds make the molecule
fold into a particular fashion.
• Disulphide bonds can be broken by
reducing agents.
 Types of bonds
• Hydrogen bond: Hydrogen bond is formed between strongly polar groups.
• A molecule that carries an unequal distribution of electrical charges is called
polar molecule.
• Electrostatic attraction between positively charged region of one molecule
and negatively charged region of a neighboring molecule forms hydrogen
bond.
• In proteins hydrogen bond is formed between H atom of NH or OH group of
one amino acid and O atom of CO group or N atom of NH group of another
amino acid.
• H is positively charged and N and O are negatively charged, so that they are
attracted forming hydrogen bond.
• Hydrogen bond can be broken by high temperature or by pH change.
• Although hydrogen bond is weak, their frequent occurrence gives molecular
stability.
Types of bonds
 Types of bonds
• Hydrophobic interactions: Interaction between
non-polar R groups of different amino acids forms
hydrophobic interactions.
• Some R groups are non polar and therefore
hydrophobic (such as those of amino acids
tyrosine and valine).
• If a polypeptide chain contains a number of these
groups and is in aqueous environment, the chain
will tend to fold into a roughly spherical shape so
that the maximum number of hydrophobic groups
come into close contact and exclude water.
• The hydrophobic groups tend to point inwards
towards the centre of roughly spherical molecule
while the hydrophilic groups face outwards into
the aqueous environment, making the protein
soluble. This is how many globular proteins fold
up.
 Structure of proteins

• There are four separate

levels of structure and
organization of proteins as
follows-
1. Primary structure
2. Secondary structure
3. Tertiary structure
4. Quaternary structure
 Structure of proteins
• Primary structure: It is the description
of basic structure of a protein.
• This includes number of polypeptide
chains in a protein as well as number
and sequence of amino acids in each
polypeptide chain.
• The sequence of amino acids of a
protein is genetically controlled by the
sequence of bases in DNA.
• Eg, insulin is a protein made up of 51
amino acids. It is made up of two
polypeptide chains held together by
disulphide bonds.
 Structure of proteins
• Secondary structure: In addition to primary structure there is a specific
secondary structure.
• Structure of protein resulting from the regular coiling or folding of polypeptide
chain is called secondary structure.
• There are three types of secondary structure:
• α helix,
• β pleated
• Collagen helix.
 Structure of proteins
• α-helix: In this type, the polypeptide chain is spirally coiled and its structure is
maintained by hydrogen bonds formed between oxygen of CO group of one
amino acid and hydrogen of NH group of next fourth amino acid.
• Thus first amino acid would be bonded to fifth amino acid, second amino acid to
sixth amino acid and so on.
• α-helical secondary structure is found in several proteins like keratin (hair),
myosin (muscle), epidermin (skin) etc.
• Β-pleated: In this type, two or more polypeptide chains get interconnected by
hydrogen bonds.
• They are arranged in parallel fashion, either running in the same direction or in
opposite directions.
• Thus a β pleated structure produces a sheet instead of a fibre or rod as in α helix.
• Hydrogen bond is formed between CO and NH groups of adjacent chains.
• β-pleated structure is found in a protein fibrion that makes silk.
Structure of proteins
 Structure of proteins
• Collagen helix: In this type, there occur three strands or polypeptide chains that
are spirally coiled around each other to form a triple helix.
• The three strands are held together by hydrogen bonds.
• Each chain is in the form of a loose helix (but not α helix).
 Structure of proteins
• Tertiary structure: It is formed by extensive
bending and folding of a polypeptide chain
forming a precise, compact globular shape.
• Tertiary structure is maintained by the
interaction of the various types of bonds
namely ionic bonds, hydrogen bonds,
disulphide bonds and hydrophobic
interactions. Hydrophobic interaction makes
proteins soluble.
• These bonds can be easily broken by high
temperature, drastic changes in pH and salts
of heavy metals. This process of degrading
the tertiary structure is known as
denaturation.
• Myoglobin, which gives red colour to
muscles, shows tertiary structure.
 Structure of proteins
• Quaternary structure: Many highly
complex proteins consists of more
than one polypeptide chains.
• The different chains are held
together by hydrophobic
interactions, hydrogen bonds and
ionic bonds. Their precise
arrangement is known as the
quartenary structure. . Hydrophobic
interaction makes proteins soluble.
• Haemoglobin, consisting of four
polypeptide chains, shows
quartenary structure.
 Classification of proteins
• On the basis of their shape, proteins are classified into fibrous and globular.
• Fibrous proteins: These are thread like proteins and consist of long parallel
polypeptide chains that are cross linked at intervals forming long fibres. They are
usually insoluble in water. They are physically tough and perform structural roles,
eg, collagen.
• Globular proteins: A protein whose molecule coils up into a globular shape is
called globular protein. Globular proteins usually curl up so that their non polar
hydrophobic R groups point into the centre of the molecule away from their
watery surroundings. Water molecules are excluded from the centre of the
protein molecule. The polar, hydrophilic R groups remain on the outside of the
molecule. Globular proteins are therefore usually soluble because water
molecules cluster around their outward pointing hydrophilic R groups. Many
globular proteins have roles in metabolic reactions, eg, enzymes.
 Collagen
• Collagen is a fibrous protein found in skin, tendons, cartilage, bones, teeth and walls
of blood vessels. It is an important structural protein.
• A collagen molecule consists of three polypeptide chains consisting largely of amino
acids glycine and proline.
• Each chain is in the shape of a helix but not an α helix as proline lacks the NH group
necessary for internal hydrogen bonds.
• The three helical polypeptide chains coil up around each other to form a triple helix.
The three strands are held together by hydrogen bonds formed between NH and CO
groups of adjacent chains. Hydrogen bonds provide stability to collagen molecule.
• Many collagen molecules unite together in bundle by covalent bonds to form
collagen fibres.
• These cross linkages provide structural support to collagen molecule, thereby making
it resistant to stretching. Therefore collagen has high tensile strength, i.e. it can
withstand large pulling forces. Thus it has an important structural role in providing
physical strength to connective tissue such as tendons.
Collagen
 Haemoglobin
• Haemoglobin, the oxygen carrier pigment found in RBC, is a globular protein.
• It is made up of four polypeptide chains. Two of these make an identical pair and are
called as alfa chains, each containing 141 amino acids and the other two make a
different identical pairs are called as beta chains each containing 146 amino acids.
• It has a quaternary structure with four polypeptide chains packing closely together by
hydrophobic interaction, hydrogen and ionic bonds forming a globular shape.
• Each polypeptide chain contains a haem group. It is a part of a haemoglobin molecule
but is not made of amino acids and calld as a prosthetic group (non-protein group).
• Each haem group contains an iron ion (ferrous, Fe++). One oxygen molecule can bind
with each iron ion. So a complete haemoglobin molecule, with four haem groups, can
carry four oxygen molecules (8 oxygen atoms) at a time making it an efficient
respiratory pigment involved in oxygen transport.
• The haem group is also responsible for the colour of haemoglobin.
Haemoglobin