PROTEINS
• Proteins are the most complex and
most diverse group of biological
compounds.
• If you weigh about 70 kg:
About 50 of your 70 kg is water.
Many and various chemicals make up
the remaining 20 kg.
About half of that, or 10 kg, is protein.
• Proteins have an astonishing range of
different functions,
– Structure: e.g. collagen (bone, cartilage,
tendon), keratin (hair), actin (muscle)
– Enzymes: e.g. amylase, pepsin, catalase,
etc (>10,000 others)
– Transport: e.g. hemoglobin (oxygen)
– Pumps: e.g. Na+K+ pump in cell
membranes
– Hormones: e.g. insulin, glucagon
– Motors: e.g. myosin (muscle), kinesin
(cilia)
– Receptors: e.g. rhodopsin (light
receptor in retina)
– Antibodies: e.g. immunoglobulins
– Blood clotting: e.g. thrombin, fibrin
• Proteins are made of amino acids.
• Amino acids are made of four elements:
C H O and Nitrogen.
• General structure of amino acid molecules:
– a central carbon atom (called the "alpha
carbon"), with four different chemical
groups attached to it:
-a hydrogen atom
-a basic amino group
-an acidic carboxyl group
-a variable "R" group (or side chain)
• There are 20 different R groups, and
therefore 20 different amino acids.
• Since each R group is different, each amino
acid has different properties: some are
hydrophobic, some are hydrophilic, and some
are ionic.
• The side chains interact with each other in a
wide variety of ways
• This in turn means that proteins can have a
wide range of properties
Peptide Bonds
• Amino acids are joined together by
peptide bonds.
• The reaction involves the formation
of a molecule of water in a
dehydration synthesis reaction:
• Two amino acids joined together:
dipeptide.
• Many amino acids: a polypeptide.
Carboxyl end
Amino acid
end
The Rules of Protein Structure
• The function of a protein is determined by its
shape.
• The shape of a protein is determined by its
primary structure(sequence of amino acids).
• The sequence of amino acids in a protein is
determined by the sequence of nucleotides in
the gene (DNA) encoding it.
Protein Structure
Primary structure:
• the sequence of amino acids. (This is
dictated by genes).
Secondary structure:
• This is the most basic level of protein folding.
• The secondary structure is held together by
hydrogen bonds between the carboxyl groups
and the amino groups in the polypeptide
backbone.
• Because it is formed by backbone interactions
it is largely independent of primary sequence
• The two most common secondary structures
are the a-helix and the b- pleated sheet.
The a-helix.
• The polypeptide chain is wound round to form
a helix.
• It is held together by hydrogen bonds
running parallel with the long helical axis.
There are so many hydrogen bonds that this
is a very stable and strong structure
The b-sheet.
• The polypeptide chain zig-zags back
and forward forming a sheet of
antiparallel strands. Once again it is
held together by hydrogen bonds.
Tertiary Structure
• This is the compact globular structure
formed by the folding up of a whole
polypeptide chain.
• Every protein has a unique tertiary
structure, which is responsible for its
properties and function.
• For example the shape of the active site
in an enzyme is due to its tertiary
structure.
• The tertiary structure is held together by
bonds between the R groups of the
amino acids in the protein, and so
depends on what the sequence of
amino acids is. There are three kinds of
bonds involved:
– hydrogen bonds, which are weak.
– ionic bonds between R-groups with
positive or negative charges, which are
quite strong.
– sulphur bridges - covalent S-S bonds
The tertiary
structure is due
to side chain
interactions and
thus depends on
the amino acid
sequence.
The final three-dimensional shape
of a protein can be classified as
globular or fibrous.
globular
structure
fibrous structure
Globular Proteins
• Globular proteins are relatively spherical
in shape.
• Common globular proteins include egg
albumin, insulin, and many enzymes
• They are somewhat soluble in water
(depending on the sequence of amino acids)
• They are easily denatured
FIBROUS PROTEINS
• Fibrous proteins form long protein filaments
with rodlike shapes.
• They are usually structural or storage
proteins.
• They are generally water-insoluble and not
easily denatured
• Fibrous proteins are usually used to
construct connective tissues: tendons, bone
matrix and muscle fiber.
Silk is secreted as a liquid. Those fibrous proteins solidify at
contact with the air to form strong and elastic polymers.
Quaternary Structure
• This structure is found in proteins containing
more than one polypeptide chain, and
simply means how the different polypeptide
chains are arranged together.
• Hemoglobin, the oxygen-carrying protein in
red blood cells, consists of four globular
subunits arranged in a tetrahedral structure.
• Immunoglobulins, the proteins that
make
antibodies,
comprise
four
polypeptide chains arranged in a Yshape. The chains are held together by
sulphur bridges.
PROTEIN DENATURATION
• Globular proteins are held in their 3D form
by a variety of bonds(hydrogen bonds, ionic
bonds, covalent bonds) between R-groups
• When these bonds are disrupted, the shape
of the protein changes…it “falls apart”
• This usually means that is cannot
accomplish its function
A number of agents can denature proteins:
• Changes in pH
• changes in salt concentration
• changes in temperature (higher temperatures
reduce the strength of hydrogen bonds)
• presence of reducing agents
• None of these agents breaks peptide bonds, so the
primary structure of a protein remains intact when
it is denatured.
When a protein is denatured, it loses its function.