Protein Structure
Primary Structure
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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.
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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.
Beta Pleated Sheets 
 A and B are antiparallel: the two strands are in opposite orientations.
 B and C are parallel: the two strands are in the same orientatio
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.
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Tertiary structure is held together by four different bonds and interactions:
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.
Ionic Bonds - If two oppositely charged 'R' groups (+ve and -ve) are found close to each
other, and ionic bond forms between them.
Hydrogen Bonds - Your typical everyday Hydrogen bonds.
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
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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.
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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.
Hemoglobin and Collagen

Hemoglobin is a water soluble globular protein which is composed of two α polypeptide
chains, two β polypeptide chains and an inorganic prosthetic hem 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.
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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 Fibers.

Collagen has many functions:
Form the structure of bones
Makes up cartilage and connective tissue
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
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Hemoglobin may be compared with Collagen as such:
Basic Shape - Hemoglobin is globular while Collagen is fibrous
Solubility - Hemoglobin is soluble in water while Collagen is insoluble
Amino Acid Constituents - Hemoglobin contains a wide range of amino acids while
Collagen has 35% of it primary structure made up of Glycine
Prosthetic Group - Hemoglobin contains a hem prosthetic group while Collagen doesn't
possess a prosthetic group
Tertiary Structure - Much of the Hemoglobin molecule is wound into α helices while
much of the Collagen molecule is made up of left handed helix structures
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