and Function
Proteinsbuilding blocks from which cells are
assembledconstitute most of the cells dry
mass.
Enzyme: Catalyzes covalent bond breakage or
formation e.g. DNA polymerasecopies DNA.
Structural protein: Provides mechanical
support to cells and tissues, e.g. collagen and
elastincommon constituents of extracellular
matrix and form fibers in tendons and
ligaments
Transport protein: Carries small molecules or
ions e.g. haemoglobin carries oxygen
Motor protein: Generates movement in cells
and tissues e.g. Myosin in skeletal muscle cells.
Storage protein: Stores small molecules or ions,
e.g. Iron is stored in the liver by binding to the
small protein ferritin.
Signal protein: Carries signals from cell to cell,
e.g. insulin.
Receptor protein: Detects signals and transmits
them to the cell's response machinery, e.g.
Rhodopsin in the retina detects light
Gene regulatory protein: Binds to DNA to
switch genes on or off, e.g. The lactose repressor
in bacteria silences the genes for the enzymes
that degrade the sugar lactose.
Special-purpose protein: Highly variable, e.g .
The antifreeze proteins of Arctic and Antarctic
fishes protect their blood against freezing.
The shape and structure of proteins
Proteins are by far the most structurally complex and
functionally sophisticated molecules known.
The Shape of a protein is Specified by its amino
acid Sequence:
Proteinsassembled from a set of 20 different amino
acids, each with different chemical properties.
A protein molecule is made from a long chain of these
amino acids, each linked to its neighbour through a
covalent peptide bondtherefore referred to as
polypeptides or polypeptide chains.
In each type of protein, the amino acids are present
in a unique order, called the amino acid sequence,
which is exactly the same from one molecule of that
protein to the next.
Each polypeptide chain consists of a
backbone that supports the different amino
acid side chains. The polypeptide backbone
is made from the repeating sequence of the
core atoms of the amino acids that form the
chain. Projecting from this repetitive
backbone are any of the 20 different amino
acid side chainsthe parts of the amino
acids that are not involved in forming the
peptide bond. These side chains give each
amino acid its unique properties. Some are
non polar and hydrophobic (water-fearing),
some are negatively or positively charged,
some are chemically reactive, and so on.
Fig. A protein, grey shows polypeptide
backbone, blue shows polar side chain
& green shows non-polar side chain
Long polypeptide chains are very flexible: many of
the covalent bonds that link carbon atoms in an
extended chain of amino acids allow free rotation of
the atoms they join. Thus proteins can in principle
fold in an enormous number of ways. Each folded
chain is constrained by many different sets of weak
non-covalent bonds that form within proteins. The
non covalent bonds that help proteins maintain their
shape include hydrogen bonds, electrostatic
attractions, and van der Waals attractions.
A fourth weak force, hydrophobic interaction, also
plays a central role in determining the shape of a
protein. In an aqueous environment, hydrophobic
molecules, including the non polar side chains of
particular amino acids, tend to be forced together to
minimize their disruptive effect on the hydrogen-
bonded network of the surrounding water molecules.
Therefore, an important factor governing the folding of
any protein is the distribution of its polar and non-
polar amino acids. The non-polar (hydrophobic) side
chainswhich belong to amino acids such as
phenylalanine, leucine, valine, and tryptophantend
to cluster in the interior of the folded protein. Tucked
away inside the folded protein, hydrophobic side
chains can avoid contact with the aqueous cytosol that
surrounds them inside a cell. In contrast, polar side
chainssuch as those belonging to arginine,
glutamine, and histidinetend to arrange themselves
near the outside of the folded protein, where they can
form hydrogen bonds with water and with other polar
molecules. When polar amino acids are buried within
the protein, they are usually hydrogen-bonded to other
polar amino acids or to the polypeptide backbone.
hydrophobic hydrogen bonds
polar core region contains can be formed
Non-polar to
side Non-polar
side chains the polar side
chains side chains
chains on the outside
of
the molecule
Folded conformation in
Unfolded polypeptide aqueous environment
Proteins fold into a conformation of
lowest energy
Proteinparticular three-dimensional structure
determined by the order of the amino acids. The final
folded structure, or conformationis determined by
energetic considerationsa protein generally folds into
the shape in which the free energy (G) is minimized.
A protein can be unfolded, or denatured, by treatment
with solvents that disrupt the non-covalent interactions
& converts the protein into a flexible polypeptide chain.
When the denaturing solvent is removed, the protein
often refolds spontaneously, or renatures, into its
original conformation which indicates that all the
information necessary to specify the three-dimensional
shape of a protein is contained in its amino acid
sequence.
Expose to a
high Remove
concentration urea
of urea
oxygen
hydrog
en
bond
carbon
hydrogen
nitrogen
nitrogen
carbon
hydrogen amino
bond acid
side sheet
hydrogen chain
nitrogen carbon
peptid
e
bond
oxygen
Helices form readily in biological
structures
A helix is a regular structure
that resembles a spiral
staircasegenerated simply
by placing many similar
subunits next to each other,
each in the same strictly
repeated relationship to the
one before. Depending on the
twist of the staircase, a helix Left- Right-
handed handed
is said to be either right-
handed or left-handed
An helix is generated when a single polypeptide
chain turns around itself to form a structurally rigid
cylinder. A hydrogen bond is made between every
fourth amino acid, linking the C=O of one peptide
bond to the NH of another. This gives rise to a
regular helix with a complete turn every 3.6 amino
acids. Short regions of helix are especially
abundant in the proteins located in cell membranes,
such as transport proteins and receptors. Those
portions of a trans-membrane protein that cross the
lipid bilayer usually form an helix that is composed
largely of amino acids with non-polar side chains.
The polypeptide backbone, which is hydrophilic, is
hydrogen-bonded to itself in the helix, and it is
shielded from the hydrophobic lipid environment of
the membrane by its protruding non-polar side
chains.
hydrophobic amino
acid hydrogen bond
side chain
Phospholipid helix
(B)
b sheet
NH2 NH2
chymotrypsin
elastase