Protein Structure

Primary Structure
Proteins are made up of polypeptide chains, which are amino acids joined together
with peptide bonds. The unique sequence of amino acids that make up a protein or
polypeptide chain is called the Primary Structure.
Primary Structure: The unique sequence of amino acids that makes up a protein or
polypeptide chain.

Peptide bonds are created by enzyme catalysed condensation reactions and broken
down by enzyme catalysed hydrolysis reactions. Breaking down proteins is important in
many areas of the body, not merely in digestion. For example, in hormone regulation,
cells that are targeted by hormones contain enzymes to break down those hormones. This
stops their effects from being permanent and allows them to be controlled.
Secondary Structure

After synthesis, polypeptide chains are folded or pleated into different shapes, called
their Secondary Structure. Two common examples of secondary structures are Alpha
Helices and Beta Pleated Sheets. Secondary structure is held together by many
Hydrogen bonds, overall giving the shape great stability.
Secondary Structure: The way in which the primary structure of a polypeptide chain
folds.

Tertiary Structure

The final 3D structure of a protein is its Tertiary Structure, which pertains to the
shaping of the secondary structure. This may involve coiling or pleating, often with
straight chains of amino acids in between.
Tertiary Structure: The final 3D structure of a protein, entailing the shaping of a
secondary structure.

Tertiary structure is held together by four different bonds and interactions:

o
Disulphide Bonds - Where two Cysteine amino acids are found together, a
strong double bond (S=S) is formed between the Sulphur atoms within the Cysteine
monomers.
o
Ionic Bonds - If two oppositely charged 'R' groups (+ve and -ve) are found
close to each other, and ionic bond forms between them.
o
Hydrogen Bonds - Your typical everyday Hydrogen bonds.
o
Hydrophobic and Hydrophilic Interactions - Some amino acids may be
hydrophobic while others are hydrophilic. In a water based environment, a globular

protein will orientate itself such that it's hydrophobic parts are towards its centre and its
hydrophilic parts are towards its edges
Tertiary structure can be broken by the action of heat. Increasing the kinetic energy
of protein with a tertiary structure makes it vibrate more, and so the bonds that maintain
its shape (which are mainly weak, non-covalent bonds) will be more likely to break. When
a protein loses its shape in this way it is said to be Denatured. Even when cool the
protein will not (or is highly unlikely to) form its original complex shape.
Proteins with a 3D structure fall
into two main types:
o
Globular - These tend to
form
ball-like
structures
where
hydrophobic parts are towards the
centre and hydrophilic are towards
the edges, which makes them water
soluble. They usually have metabolic
roles,for example: enzymes in all
organisms, plasma proteins and
antibodies in mammals.
o
Fibrous - They proteins
form long fibres and mostly consist of
repeated sequences of amino acids
which are insoluble in water. They
usually have structural roles, such as:
Collagen in bone and cartilage,
Keratin in fingernails and hair.

Quaternary Structure

Some proteins are made up of multiple polypeptide chains, sometimes with an

inorganic component (for example, a haem group in haemoglogin) called a Prosthetic
Group. These proteins will only be able to function if all subunits are present.
Quaternary Structure: The structure formed when two or more polypeptide chains join
together, sometimes with an inorganic component, to form a protein.
Haemoglobin and Collagen

Haemoglobin is a water soluble globular protein which is composed of two

polypeptide chains, two polypeptide chains and an inorganic prosthetic haem group. Its
function is to carry oxygen around in the blood, and it is facilitated in doing so by the
presence of the haem group which contains a Fe2+ ion, onto which the oxygen molecules
can bind.

Collagen is a fibrous protein consisting of three polypeptide chains wound around

each other. Each of the three chains is a coil itself. Hydrogen bonds form between these
coils, which are around 1000 amino acids in length, which gives the structure strength.
This is important given collagen's role, as structural protein. This strength is increased by
the fact that collagen molecules form further chains with other collagen molecules and
form Covalent Cross Links with each other, which are staggered along the molecules to
further increase stability. Collagen molecules wrapped around each other form Collagen
Fibrils which themselves form Collagen Fibres.

Collagen has many functions:

o
Form the structure of bones
o
Makes up cartilage and connective tissue

o
o
o
o
o
o

Prevents blood that is being pumped at high pressure from bursting the walls
of arteries
Is the main component of tendons, which connect skeletal muscles to bones
Haemoglobin may be compared with Collagen as such:
Basic Shape - Haemoglobin is globular while Collagen is fibrous
Solubility - Haemoglobin is soluble in water while Collagen is insoluble
Amino Acid Constituents - Haemoglobin contains a wide range of amino
acids while Collagen has 35% of it primary structure made up of Glycine
Prosthetic Group - Haemoglobin contains a haem prosthetic group while
Collagen doesn't possess a prosthetic group
Tertiary Structure - Much of the Haemoglobin molecule is wound into
helices while much of the Collagen molecule is made up of left handed helix structures