PROTEINS

Projecting from the polypeptide backbone are the

What is Protein?  amino acid side chains – the part of the amino acid
• Polymer built from amino acids that provides cells that is not involved in forming peptide bonds.
with their shape and structure and performs most of The side chain gives an amino acid its unique
their activities.  properties: some are nonpolar and hydrophobic,
• A biological macromolecule containing at least 30 to some are positively or negatively charged, some can
50 amino acids joined by peptide bonds  be chemically reactive and so on.
• A protein molecule is made from a long chain of
amino acids held by covalent peptide bond. 
• Proteins therefore referred as polypeptides, and
their amino acid chains are called polypeptide chains.
• In each type of protein, the amino acids are present
in a unique order, called the amino sequence, which
is exactly the same from one molecule of that protein
to the next.

20 essential amino acids

Amino Acid Monomers

Amino acids are organic
molecules with carboxyl and
amino groups Amino acids
differ in their properties due
to differing side chains,
called R groups

Amino Acid Polymers

Amino acids are linked by peptide bonds
A polypeptide is a polymer of amino acids Secondary structure, found in most proteins, consists
Polypeptides range in length from a few to more than of coils and folds in the polypeptide chain
a thousand monomers Tertiary structure is determined by interactions
Each polypeptide has a unique linear sequence of among various side chains (R groups)
amino acids, with a carboxyl end (C-terminus) and an Quaternary structure results when a protein consists
amino end (N-terminus) of multiple polypeptide chains 
• Primary structure, the sequence of amino acids in a
protein, is like the order of letters in a long word 
• Primary structure is determined by inherited genetic
information

Protein Structure and Function

A functional protein consists of one or more
polypeptides precisely twisted, folded, and coiled into
a unique shape

• The coils and folds of secondary structure result

from hydrogen bonds between repeating constituents
of the polypeptide backbone 
• Typical secondary structures are a coil called an 
helix and a folded structure called a  pleated sheet
• The sequence of amino acids determines a
protein’s three-dimensional structure 
• A protein’s structure determines its function

Four Levels of Protein Structure

The primary structure of a protein is its unique
sequence of amino acids
 Sickle-Cell Disease: A Change in Primary
Structure
A slight change in primary structure can affect a
protein’s structure and ability to function
Sickle-cell disease, an inherited blood disorder,
results from a single amino acid substitution in the
protein hemoglobin

• Tertiary structure is determined by interactions

between R groups, rather than interactions between
backbone constituents 
• These interactions between R groups include
hydrogen bonds, ionic bonds, hydrophobic
interactions, and van der Waals interactions 
• Strong covalent bonds called disulfide bridges may
reinforce the protein’s structure
What Determines Protein Structure? 
• In addition to primary structure, physical and
chemical conditions can affect structure 
• Alterations in pH, salt concentration, temperature, or
other environmental factors can cause a protein to
unravel 
• This loss of a protein’s native structure is called
denaturation 
• A denatured protein is biologically inactive

• Quaternary structure results when two or more Denaturation of proteins by heat or by deviation of pH
polypeptide chains form one macromolecule  from the optimum.
• Collagen is a fibrous protein consisting of three • The three-dimensional conformation of proteins is
polypeptides coiled like a rope  stabilized by bonds or interactions between R groups
• Hemoglobin is a globular protein consisting of four of amino acids within the molecule. Most of these
polypeptides: two alpha and two beta chains bonds and interactions are relatively weak and they
can be disrupted or broken. This results in a change
to the conformation of the protein, which is called
denaturation.
• A denatured protein does not normally return to its
former structure – the denaturation is permanent.
Soluble proteins often become insoluble and form a
precipitate.
• Heat can cause denaturation: vibrations within the
molecule breaks intramolecular bonds or interactions.
• Extremes of pH can cause denaturation: charges on
R groups are changed, breaking ionic bonds within
the protein or causing new ionic bonds to form.
• The background image shows white smokers, a
particular kind of hydrothermal vent which produces
very hot carbon dioxide gas. These vents can be • Protein functions include structural support, storage,
found deep in oceans and produce temperatures in transport, cellular communications, movement, and
excess of 100 °C, but life can still be found around defense against foreign substances
them.
• Thermophiles are organisms (often archea or Types of Proteins
eubacteria) that live in relatively hot conditions (45
to122 °C). In order that they can survive their
proteins are stable at the higher than normal
temperatures they experience.

Protein Folding in the Cell 

• It is hard to predict a protein’s structure from its
primary structure 
• Most proteins probably go through several stages
on their way to a stable structure 
• Chaperonins are protein molecules that assist the
proper folding of other proteins 
• Diseases such as Alzheimer’s, Parkinson’s, and
mad cow disease are associated with misfolded
proteins

• Scientists use X-ray crystallography to determine a

protein’s structure 
• Another method is nuclear magnetic resonance
(NMR) spectroscopy, which does not require protein
crystallization 
• Bioinformatics uses computer programs to predict
protein structure from amino acid sequences

Proteins include a diversity of structures,

resulting in a wide range of functions 
• Proteins account for more than 50% of the dry mass
of most cells 
 (Polypeptide)
• The order / sequence of the amino acids of which
the protein is composed
• Formed by covalent peptide bonds between
adjacent amino acids
• Controls all subsequent levels
of structure

• The chains of amino

acids fold or turn
upon themselves
• Held together by
hydrogen bonds
between (non-
adjacent) amine (N-
H) and carboxylic (C-
O) groups
• H-bonds provide a level of structural stability
• Fibrous proteins

• The polypeptide folds and coils to

form a complex 3D shape
• Caused by interactions between R
groups (H-bonds, disulphide
bridges, ionic bonds and
hydrophilic / hydrophobic
interactions)
• Tertiary structure may be important
for the function (e.g. specificity of
active site in enzymes)
• Globular proteins
• Enzymes are a type of protein that acts as a
catalyst to speed up chemical reactions  • The interaction between
• Enzymes can perform their functions repeatedly, multiple polypeptides or
functioning as workhorses that carry out the prosthetic groups • A
processes of life prosthetic group is an
inorganic compound involved
ADDITIONAL INFORMATION in a protein (e.g. the heme
The sequence and number of amino acids in the group in haemoglobin)
polypeptide is the primary structure. The secondary • Fibrous and Globular
structure is the formation of alpha helices and beta proteins
pleated sheets stabilized by hydrogen bonding. The
tertiary structure is the further folding of the : although you don’t need to be able to outline the
polypeptide stabilized by interactions between R different levels of structure for knowing of them helps
groups. The quaternary structure exists in proteins to understand the difference between globular and
with more than one polypeptide chain. fibrous proteins. This is though required knowledge
for AHL
The four levels of
protein structure
The level a protein
conforms to is The amino acid sequence determines the three-
determined by it’s amino dimensional conformation of a protein.
acid sequence.
Proteins are commonly described as either being
fibrous or globular in nature.
Fibrous proteins have structural roles whereas • Found in high concentrations in leaves and algal
globular proteins are functional (active in a cell’s cells
metabolism).
Insulin
• A hormone – signals many cells (e.g. liver cells) to
absorb glucose and help reduce the glucose
concentration of the blood.
• Affected cells have receptor (proteins) on their
In globular proteins the hydrophobic R groups are surface to which insulin can (reversibly) bind to.
folded into the core of the molecule, away from the • Secreted by β cells in the pancreas and transported
surrounding water molecules, this makes them by the blood.
soluble. In fibrous proteins the hydrophobic R groups The pancreas of type I diabetics don’t produce
are exposed and therefore the molecule is insoluble. sufficient insulin therefore they must periodically
inject synthetically produced insulin to correct their
Living organisms synthesize many different proteins blood sugar concentration.
with a wide range of functions.
Usage of proteins Immunoglobulins
Nothing can compare with the versatility of proteins. • Also known as antibodies.
Their functionality and usage in organisms is • Two antigen (a molecule on the pathogen which
unrivalled. provokes an immune response) binding sites - one on
each ‘arm’
• Binding sites vary greatly between immunoglobulins
(hypervariable) to enable them to respond a huge
range of pathogens.
• Other parts of the immunoglobulin molecule cause a
response, e.g. acting as a marker to phagocytes
(which engulf the pathogen)
• Key examples are outlined in more detail.
• Although a key example spider silk is not mentioned
above as the table refers to uses within the organism

Biotechnologically has allowed us to use proteins in

industry examples are:
• enzymes for removing stains in clothing detergent Rhodopsin
• monoclonal antibodies for pregnancy tests • A pigment that absorbs light
• insulin for treating diabetics • Membrane protein of rod cells of the retina (light
• Disease treatments sensitive region at the back of the eye)
Genetically modified organisms are often used as to • Rhodopsin consists of the opsin polypeptide
produce proteins. surrounding a retinal prosthetic group
• retinal molecule absorbs a single photon of light ->
Rubisco, insulin, immunoglobulins, rhodopsin, changes shape -> change to the opsin -> the rod cell
collagen and spider silk as examples of the range of sends a nerve impulse to the brain
protein functions. • Even very low light intensities can be detected.
Rubisco
• Full name ribulose bisphosphate carboxylase Collagen
• Enzyme - catalyses the reaction that fixes carbon • A number of different forms
dioxide from the atmosphere • All are rope-like proteins made of three polypeptides
• Provides the source of carbon from which all carbon wound together.
compounds, required by living organisms, are • About a quarter of all protein in the human body is
produced. collagen
• Forms a mesh of fibres in skin and in blood vessel
walls that resists tearing.
• Gives strength to tendons, ligaments, skin and
blood vessel walls.
• Forms part of teeth and bones, helps to prevent
cracks and fractures to bones and teeth

• Different types of silk with different functions

• Dragline silk is stronger than steel and tougher than
Kevlar
• When first made it contains regions where the
polypeptide forms parallel arrays (bottom)
• Some regions seem like a disordered tangle
(middle) • When the stretched the polypeptide
gradually extends, making the silk extensible and
very resistant to breaking.