1. STUDYING THE INTERACTIONS OF MOLECULES
Recall that a molecule is composed of 2 or more atoms chemically joined together.
There are different types of bonds that can hold elements together.
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

2. VALENCE ELECTRONS: Electrons in the outermost orbital that determine an atoms chemical behaviour.
Noble gases – have full outer orbitals/thus they do not gain, lose, or share electrons (i.e. don’t participate in chemical reactions.)
All other elements attempt to gain, lose, or share valence electrons to achieve stable electron configurations like noble gases.
HENCE chemical reactions occur and chemical bonds form.

3. CHEMICAL BONDING (Intramolecular Bonding = Forces that hold atoms together within a molecule.)
IONIC
transfer e-
electrostatic attraction between metal cation and non-metal anion
Form ionic solids
Ionic solids form crystals that can pull apart in water.
All ionic compounds are water soluble.
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  Na e- (oxidation= LEO loss of electrons)
O + 2 e-  O2- (reduction = GER gain of electrons)

5. CHEMICAL BONDING Covalent Bonding
Share electrons
Two non-metal nuclei attract e- at the same time and thus they are shared.
Form molecules
Electrons can be shared equally forming a non-polar covalent bond or unequally forming a polar covalent bond.

6. ELECTRONEGATIVITY
Electronegativity – the measure of the tendency of an atom to attract electrons.
See figure 7 on page 14 for table of electro- negativities
Describe the electronegativity of the biological atoms (C, H, O, N, S, P)
O, N, and Cl are atoms with high electronegativities
C, H, and P are examples of atoms with lower electronegativities

7. Polar Covalent Bonds
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- )
The atom with the lower electronegativity becomes a partial positive charge (δ+)

8. Non-polar covalent bonds
When bonds are formed between atoms that have similar electronegativities the electrons are shared fairly equally between the atoms.
Examples: diatomic molecules or the bonds between carbon and hydrogen atoms.

9. ELECTRONEGATIVITY AND CHEMICAL BONDING
Electronegativity difference (∆En) rule:
NONPOLAR POLAR COVALENT IONIC
0  > 1.7
e- shared e- shared e-
equally unequally transferred

10. Polarity or charge of biological molecules greatly affects their behaviors and functions within a cell.

11. INTERMOLECULAR BONDING
“between” molecules (attractive forces that allow molecules to associate together)
weaker than intramolecular
Determine the state of substances at given temperature and pressures.
Collectively called vanderWaals forces.
VanderWaal has “3 children” collectively known as:
London’s Forces
Hydrogen Bonding
Dipole dipole interactions (hydrophobic interactions)

12. INTERMOLECULAR BONDING
The two intermolecular interactions that are important for biological systems are:
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!

13. INTERMOLECULAR BONDING
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 like)
Since water is polar, all polar molecules are considered “water loving” or hydrophilic.
Non-polar molecules don’t mix with water and are called “water hating” or hydrophobic.
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.

14. MOLECULAR POLARITY Molecular polarity depends on
The polarity of individual bonds (which depends in part upon functional groups for biological molecules)
and
the shape of the molecule (this depends upon the distribution of electron orbitals)

15. ELECTRON ORBITALS
It is impossible to know exactly where electrons are at any given time
Scientists can determine locations where electrons are most likely to be found
These spaces are called orbitals. (s,p,d,f) see fig.4 pg.11

16. Hybridization of orbitals
When atoms form covalent bonds the orbitals hybridize.

17. Hybridization of orbitals

18. Hybridization of orbitals
Hybridization pushes bonding and non-bonding electrons as far apart as possible
Each hybridized orbital will hold 2 e-
To simplify we will assume that biological molecules will only possess up to 4 electron pairs (4 sp3 hybrid orbitals)

19. Shape depends on the number of bonding and non-bonding pairs of electrons. (see table 5 on page 15)

20. See table 5 on page 15
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
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

22. REMEMBER
The polarity of molecules greatly affects their behavior and function within a cell.