STUDYING THE INTERACTIONS
n Recall that a molecule is composed of 2 or
more atoms chemically joined together.
n There are different types of bonds that can
hold elements together.
n Biological molecules are organic or carbon
based where carbon is bonded to carbon or
hydrogen and may also include atoms of
nitrogen, oxygen, phosphorus, and sulfur
VALENCE ELECTRONS: Electrons in
the outermost orbital that determine an
atoms chemical behaviour.
n Noble gases – have full outer orbitals/thus they
do not gain, lose, or share electrons (i.e. don’t
participate in chemical reactions.)
n All other elements attempt to gain, lose, or
share valence electrons to achieve stable
electron configurations like noble gases.
n HENCE chemical reactions occur and chemical
(Intramolecular Bonding = Forces that hold atoms
together within a molecule.)
n transfer e-
n electrostatic attraction between metal cation and non
n Form ionic solids
n Ionic solids form crystals that can pull apart in
n All ionic compounds are water soluble.
n Recall – Ions = atoms with a charge.
Cation(metals) = when atoms lose e- they become positive.
Anion(non-metals) =when atoms gain e- they become negative.
Ionic Bond = attraction between a cation and an anion
Example: Na à Na1+ + 1 e- (oxidation= LEO loss of electrons)
O + 2 e- à O2- (reduction = GER gain of electrons)
2. Covalent Bonding
n Share electrons
n Two non-metal nuclei attract e- at the
same time and thus they are shared.
n Form molecules
Electrons can be shared equally forming a non-polar
covalent bond or unequally forming a polar covalent
n Electronegativity – the measure of the
tendency of an atom to attract electrons.
n See figure 7 on page 14 for table of electro-
n Describe the electronegativity of the
biological atoms (C, H, O, N, S, P)
n O, N, and Cl are atoms with high
n C, H, and P are examples of atoms with lower
Polar Covalent Bonds
n When 2 atoms with significantly different
electronegativities share electrons those electrons are
more strongly attracted to the atom with the higher
electronegativity and cause that atom to have a
partial negative charge.(δ- )
n The atom with the lower electronegativity becomes a
partial positive charge (δ+)
Non-polar covalent bonds
n When bonds are formed between atoms that
have similar electronegativities the electrons
are shared fairly equally between the atoms.
n Examples: diatomic molecules or the bonds
between carbon and hydrogen atoms.
Electronegativity difference (∆En) rule:
NONPOLAR POLAR COVALENT IONIC
0à 0.5 0.6 à 1.6 > 1.7
e- shared e- shared e-
equally unequally transferred
n Polarity or charge of biological
molecules greatly affects their behaviors
and functions within a cell.
n Intermolecular bonding
n “between” molecules (attractive forces that allow
molecules to associate together)
n weaker than intramolecular
n Determine the state of substances at given temperature
n Collectively called vanderWaals forces.
n VanderWaal has “3 children” collectively known as:
n London’s Forces
n Hydrogen Bonding
n Dipole dipole interactions (hydrophobic interactions)
The two intermolecular interactions that are
important for biological systems are:
1. Hydrogen bonding – strong – partial positive
(δ+) hydrogen atoms are attracted to the
partially negative (δ-) N, O, or F of another
atom. (H-F, O-H, N-H).
This is extremely important in biological systems
as water molecules form hydrogen bonds with
one another. All cells are aqueous environments.
So hydrogen bonds between biological molecules
and water are very important!
2. Dipole-dipole Forces (Hydrophobic Interactions)
weak – occurs between polar molecules (δ+
side of one molecule is attracted to the δ- side
of another molecule. Remember opposites
attract!!). Thus polar molecules have a
tendency to mix and interact! (Like dissolves
1. Since water is polar, all polar molecules are
considered “water loving” or hydrophilic.
2. Non-polar molecules don’t mix with water and are
called “water hating” or hydrophobic.
3. The natural clumping together of non-polar
molecules is known as the hydrophobic effect. This
plays a central role in how cell membranes form or
the 3-dimensional shapes of proteins.
Molecular polarity depends on
1. The polarity of individual bonds (which
depends in part upon functional
groups for biological molecules)
2. the shape of the molecule (this
depends upon the distribution of
n It is impossible to know
exactly where electrons
are at any given time
n Scientists can determine
electrons are most likely
to be found
n These spaces are called
orbitals. (s,p,d,f) see fig.4
Hybridization of orbitals
n When atoms form
covalent bonds the
Hybridization of orbitals
Hybridization of orbitals
n Hybridization pushes bonding and non-
bonding electrons as far apart as
n Each hybridized orbital will hold 2 e-
n To simplify we will assume that
biological molecules will only possess up
to 4 electron pairs (4 sp3 hybrid orbitals)
Shape depends on the number of
bonding and non-bonding pairs of
electrons. (see table 5 on page 15)
See table 5 on page 15
n If the molecule has a symmetrical shape
(linear, trigonal planar, or tetrahedral) then if
all bonds are the same (can be polar or non-
polar) the molecule will overall be non-polar
n If the molecule has an asymmetrical shape
(bent, or pyramidal) and the bonds are polar
then the molecule will be polar. However if
the bonds are non-polar then the molecule
will be non-polar
The polarity of molecules greatly affects
their behavior and function within a cell.