Lecture 1
BIOCHEMISTRY - INTRODUCTION
REVIEW
 At home review the following definitions (p. 4 txb):
 element;
 compound;
 protons; neutrons; electrons;
 valence electrons;
 isotopes;
 ions (cations and anions);
 ionic bond;
 covalent bond
WHAT IS BIOCHEMISTRY?
 Field of study that deals with properties and interactions of
molecules and atoms with the biological life forms, (inside the cells
and other living organisms)
 Study of biologically important molecules
 Currently, there are million reactions going on in our body, that we
are not even aware of. Our cells carry life function automatically.
 For the past two hundred years biologists studied the cells and
organisms and have discovered that chemical reactions are the
basis of every biological process.
EXAMPLES OF CHEMICAL REACTIONS
RELATED TO LIVING ORGANISMS
 Most animals die in several weeks without food, a few
days without water, and a few minutes without oxygen.
 Many species of archaebacteria will die in the presence
of oxygen.
 Without a daily intake of magnesium, body muscles
become sore and weak, the human brain fails to work
properly, and plants turn yellow and die.
 The common herbicide 2,4-D stimulates weeds to grow
in such an uncoordinated fashion that they literally grow
themselves to death. (Which plant hormone stimulates
growth?)
MORE EXAMPLES
 The anti-cancer drug, Taxol, stops cell growth by
disrupting spindle fibre function during mitosis.
 Tadpoles transform into frogs and caterpillars into
butterflies through chemical changes
 Leaves change colour in the fall
 Hunger is caused by variety of chemical changes in our
body and chemical signaling to our brain when we
need food.
 When we are scared, chemical reactions in our muscles
allow us to run away from danger.
BASIC CONCEPTS OF CHEMISTRY
Intramolecular vs. intermolecular forces of
attraction
 Intra – inside
 Intramolecular forces of attraction are the bonds that hold the
atoms within the molecule together. There are two types: ionic and
covalent.
IONIC BOND
 In ionic bond there is an electrostatic attraction between oppositely
charged atoms. Eg. Sodium chloride, Magnesium Fluoride.
 Show Lewis diagram for these two molecules and the chemical structures.
COVALENT BOND
 Electrostatic attraction between the nuclei and the valence
electrons of the neutral atoms. “sharing of electrons”
 Examples: water, carbon dioxide, sugar (glucose)
 Show Lewis diagram for these two molecules and the chemical
structures.
SUGAR CUBE
INTERMOLECULAR FORCES OF
ATTRACTION (Van Der Waals forces)
 These are the forces between the molecules:
 (Note: the molecules are neutral = i.e. charge = 0)
 London forces (London dispersion forces)
 dipole–dipole forces
 hydrogen bonds (H-bonds)
MOLECULAR POLARITY
 As you recall each atom has its own electronegativity value
(based on experimental results).
 This value indicates the strength of attraction of the electrons
to the nucleus.
 In a molecule, when electrons are unequally shared (due to
one atom having a higher electronegativity value), the
molecule tends to have one side partially more positive and one
side partially more negative.
 (Note: the molecule is still neutral).
 Greek letter delta (d) denotes a partial charge:
 d-  is to that side of the molecule where the electron pair spends
more time in.
 d+  is to the side where the electron pair spends less time in.
DIPOLE-DIPOLE FORCES
Attraction between molecules where the
electronegative side is attracted to the positive
side.
Weak forces of attraction.
Example of dipole-dipole forces: Hydrogen
bonds
HYDROGEN BOND
 Hydrogen bond – is a specific dipole-dipole attraction
between molecules containing:
H—N
H—O
H—F
 It is the STRONGEST of the intermolecular forces.
 Why do you think hydrogen bond happens only with N,
O and F?
 because they are most electronegative.
H-Br, NOT A HYDROGEN BOND
Note:
H—Br also has uneven distribution of charges,
and will have some kind of intermolecular force,
but it is not hydrogen bond, because not N, O
and F! It is just dipole-dipole type of force.
LONDON FORCES
 This is the force between the molecules that is always present (due to
momentary electron shift).
 These are week attractive forces which result from temporary dipolar
attractions between the neighbouring atoms.
 Important because they are the only forces of attraction between:
 adjacent noble gas atoms Eg. Kr, He
 adjacent covalently-bonded non-polar molecules
 ALWAYS present even in species of covalent or ionic bonding
 WEAKEST type of bonding known
 The greater the atomic number of the atom, the stronger the London
force it experiences. (increase in number of electrons  increase in
London Forces
London Forces
 Methane is a gas (weak London forces) and octane is a
liquid (stronger London forces than those between
methane molecules).
WATER IS UNIQUE
 Water is a universal solvent. It is called that because a lot
of substances are dissolved in it.
 Sodium chloride molecule dissolves in water while the
ionic lattice disassociates
 Water is able to break the ionic bonds.
 Can it dissolve all molecules?
 No. Exception is for molecules that are insoluble in water. Eg. Calcium
carbonate, Silver acetate etc. (see solubility rules from Chem grade
11).
MISCIBLE OR IMMISCIBLE
 When liquids are dissolved with each other, they are
miscible. Eg. ethanol in water; ethylene glycol in water.
 Gasoline and oil are immiscible with water.
 Gasoline and oil are miscible with each other. “like
dissolves like”.
FORCES OF ATTRACTION IMPORTANCE
IN BIOLOGY
 O2 gas and CO2 gas cannot form hydrogen bonds with
water (non polar)
 insoluble or only slightly soluble.
 Therefore, need hemoglobin to carry the oxygen in the blood,
rather than oxygen to be dissolved in the plasma of the blood.
 Fats and oils do not form hydrogen bonds with water.
 Water molecules from hydrogen bonds with each other and
exclude that non polar molecules, such as fat and oil. Hydrophobic
molecules
 Oil floats on water, because it is less dense than water, but it is not
dissolving in water because it is non polar (hydrophobic).
ADHESION - COHESION
 Cohesion
 hydrogen forces between the water molecules. Water molecules
“cling” to each other.
 High surface tension – the shape of a dew on a leaf.
 A water strider walks on the surface of the water.
 Adhesion
 water molecules form hydrogen bonds with other polar molecules
 capillary action - the water is transported from roots to the top of the trees
through the thin xylem vessels.
HEAT ABSORPTION
 Specific high heat capacity
 hydrogen bonding in water causes water to absorb a large amount of heat before its
temperature increases.
 And vise-versa: causes it loose large amount of heat before its temperature
decreases.
 This allows organisms to maintain a constant body temperature.
 Specific high heat of vapourization
 it takes more energy to break the hydrogen bond (the strongest bond of the
3 van der Waals forces)
 When water vapourizes (liquid  gas) it takes away a lot of heat.
 This is how organisms, including humans, cool off: sweating – cools off the
skin, panting – turning water to vapour – cools off some animals.
DENSITY SOLID < DENSITY LIQUID
 Water forms crystalline structure bellow 0oC (ice). The hydrogen
bonds spread the water molecules apart in a hexagonal solid
structure. Because the molecules are further apart, the density
decreases.
 This makes the solid water (ice) to float on liquid water. Which allows
aquatic organisms and fish to survive in the winter.
ACID-BASE REACTIONS
 Pure water never contains only H2O molecules.
 At 25°C, two H2O molecules in every 550 million react
with each other.
 One H2O molecule transfers an H+ ion to the other H2O
molecule.
 This produces an OH- (hydroxide) ion and an H3O(hydronium) ion.
 Because hydroxide and hydronium ion amount is equal
– the water is said to be neutral.
ACIDIC SOLUTION
 Sour taste
 Conducts electricity
 Turns blue lithmus paper red
 pH paper – red colour (strong acid)
 H3O- ion concentration determines the strength of an
acid
BASIC SOLUTION
 Bitter taste
 Slippery feel
 Conducts electricity
 Turns red lithmus to blue
 pH paper – dark blue colour (strong base)
 OH- ion concentration determines the strength of a base
NEUTRALIZATION REACTION
 When acid and base solutions are mixed, neutralization reaction occurs, forming
water and salt:
 HCl (aq) + NaOH (aq)  H2O (l) + NaCl (aq)
pH SCALE
 pH is measuring the concentration of hydronium ions in a solution.
Where 7 is said to be neutral, i.e. concentration of [H+] in water.