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Assignment 2 Proteins

At the end of this assignment

preparation you will be able to :
Describe the general structure of an amino acid
Describe how condensation reactions result in
the formation of peptide bonds linking together
amino acids to form polypeptides.
Understand the primary, secondary, tertiary and
quaternary structure of proteins
Explain how the structure of proteins links to
their functions.

It is Greek for
of first

What does

Where in your body would you

find proteins?
Muscles (actin and myosin)
Hair and nails (keratin)
Digestive system - enzymes
Cell membranes
In ligaments, bones and tendons
Immune system antibodies are

Carbon, Hydrogen, Oxygen, Nitrogen
and sometimes Sulphur
Polymers made up of Amino acids
20 commonly occurring amino acids

Structure of an amino acid



All amino acids have the same overall structure

only the R group changes!

the variable group in

amino acids
If the atomic R
group is POLAR,
the amino acid
will be SOLUBLE
in water.
If the atomic R
group in NONPOLAR, the amino
acid will be

Examples of amino acids

Amino acid

R group






How do amino
acids join
together? And
what do they
Hint: Think back to

Atomic R
Lysine (Lys)



Alanine (Ala)

How is a protein

This is a CONDENSATION reaction.

The amino acids are now called
amino acid residues
Three amino acids = tripeptide

Polypeptide chain

Many amino acids can be joined together

to form a polypeptide

In the same way as carbohydrates, the
peptide bond between two amino acids
can be broken in hydrolysis by the
addition of water. This produces two
separate amino acids again.

Structure of Protein

Primary Structure

Long, straight chain of amino acids joined together.

The specific sequence of amino acids determines the function
of the protein

The primary structure can be

shown using 3 letter abbreviations
for the amino acids, e.g.

Importance of primary
Determines ultimate shape and
function of the protein
A change in any one amino acid in
the primary sequence, could lead
to change in shape or function of
the protein
Therefore, proteins shape is VERY
SPECIFIC to its function

Secondary Structure

The secondary structure is the folding of the chain of amino

The hydrogen bonds form between =O on one amino acid
residue and the H of another.
This is an intramolecular force.

Tertiary structure

The specific tertiary structure of a protein is the

specific folding of the secondary structures.
The structure is held together by HYDROGEN, IONIC, and
sometimes DISULPHIDE (S-S) bonds.

Tertiary structure of
The polypeptide chains often fold to
give unique complex 3D structure of
This is maintained by:
Weak hydrogen bonds (easily
Stronger ionic bonds formed
between carboxyl and amino
groups (can be broken by changes
in pH)
Even stronger disulfide bonds (not
easily broken). These covalent
bonds form between R groups that

Bonds also form between nonpolar (hydrophobic) R groups.

Quaternary structure of
Some proteins consist
of more than one
polypeptide chain or
polypeptide chains and
non-protein (prosthetic)
groups (eg:
haemoglobin contains
iron), which gives a
fourth level of structure
This shape is created
when the different
chains bind together to
form whole protein

Fibrous and Globular

Fibrous-structural roles. E.g Keratin
in nails, Collagen in bone and
Globular-enzymes, antibodies &
E.g. Insulin, haemoglobin.

Fibrous protein
Insoluble because Rgroups are non-polar
Secondary structure
of long polypeptide
chains forming
fibres (alpha helix)
or sheets (beta
pleated sheet).
Fibres give strength,
sheets flexibility.

Made up from 3
chains (alpha
helix) twisted
together giving a
strong structure.

Globular Proteins
Highly folded and coiled with more than 1
polypeptide chain (complex tertiary
Each chain is called a subunit
Hydrogen, ionic and sulfide bonds hold its
Soluble with a specific tertiary structure
as hydrophilic R groups are on the outside

Haemoglobin is a conjugated
quaternary protein comprising:
two alpha-globulins
two beta-globulins
four haem groups, each with
an iron atom at its core
It is the iron atoms which bind

Linking structure to function

Haemoglobin has 4 heam groups that
contain iron to carry the oxygen.
The binding of the first oxygen molecule
changes the shape of the molecule, making
it easier for the second oxygen molecule to
The binding to oxygen only happens at high
partial pressure of oxygen (in the lungs) and
reverses at low partial pressures (in the
tissues). So oxygen is released in the tissues
for use in respiration.

So to function efficiently, haemoglobin must attract

oxygen under certain conditions, but lose it under
other conditions.
Loading/unloading is a reversible reaction, in
which one haemoglobin (Hb) can attract up to 4
oxygen molecules:

Hb + 4O2



Keratin in hair

A hair

Keratin forms nails and hair.

The polypeptide chain has hydrogen bonds
between the amino acid residues that hold it
into an alpha helix secondary structure.
Hydrogen bonds, disulphide bridges and
hydrophobic interactions hold the polypeptide
chains together forming tough, insoluble

The hydrogen bonds in the secondary

structure are easily broken if hair is pulled.
This allows hair to stretch a little, particularly
when heat is applied a characteristic that is
used in styling.
The primary structure has a leucine (amino
acid) approximately every 7th residue. These
form the hydrophobic interactions.
Many cysteine molecules allow the formation
of disulphide bridges. Nail and hooves have
more cysteine, making them stronger.