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BASIC CELL
BIOLOGY
I CHEMISTRY of LIFE
CHEMICAL BONDS, INTERMOLECULAR
FORCES, PROPERTIES OF WATER,
BUFFER SOLUTIONS
Lecture 3
CHEMICAL BONDS, INTERMOLECULAR
FORCES, PROPERTIES OF WATER,
BUFFER SOLUTIONS
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Covalent bond
Van der Waals forces
Hydrophobic interactions
Hydrogen bond
Biologically important properties of water
pH, acids and bases
Buffer solutions
Chemical bond
Lecture 3
In forming chemical bonds,
atoms donate, acquire, or share
electrons.
Chemical bond : ionic bond
Lecture 3
The electron from the
outer shell of sodium
atom is transferred to the
outer shell of the chlorine
atom.
The
number
of
the
electrons which can be
donated
or
accepted
determine the valence of
the atom.
Sodium and chlorine are
monovalent atoms.
Chemical bond : ionic bond
Lecture 3
Not only the atoms, also functional
groups can be ionised through donation
or acceptance of the proton.
Chemical bond : ionic bond
Lecture 3
Ionic bond participates in the formation of the
secondary structure of the proteins
Lecture 3
Chemical bond : covalent bond
Sharing of the pair of electrons through
formation of the common electron shells
One common pair of the electrons
Formation of the bond
Structural formula
Energy: ~80 kcal/mole
Lecture 3
Chemical bond : covalent bond
Sharing of the pair of electrons through
formation of the common electron shells
Two common pairs of the electrons
Formation of the bond
Structural formula
Energy: ~150 kcal/mole
Lecture 3
Chemical bond : covalent bond
Sharing of the pair of electrons through
formation of the common electron shells
Three common pairs of the electrons
Formation of the bond
Structural formula
Energy: ~200 kcal/mole
Lecture 3
Chemical bond : covalent bond
Formation of the covalent bond between
different atoms: carbon and hydrogen
Formation of the bond
Structural formula
Spatial structural formula
Lecture 3
Chemical bond : covalent bond
Formation of the covalent bond between
different atoms: carbon and oxygen
Formation of the bond
Carbon atom forms
four, oxygen atom
forms two common
pairs of electrons.
Structural formula
Lecture 3
Chemical bond : covalent bond
Formation of the covalent bond between
different atoms: carbon and oxygen
Formation of the bond
Nitrogen atom forms
three, hydrogen atom
forms one common
pairs of electrons.
Structural formula
Spatial structural formula
Chemical bond : covalent bond
Lecture 3
Covalent bonds make the backbone of the organic
molecules and ensure their stability
Chemical bonds
Lecture 3
The valence of the atom at ionic bonding is
determined by the number of donated or
accepted electrons.
The valance of the atom at covalent bonding is
dertemined by the number of formed common
electron pairs.
Intermolecular forces
Van der Waals forces
Lecture 3
The movement of the electrons in the molecule
or atom creates instant non-uniformity of the
charge distribution, the molecule or the atom
gets polarised, instant dipole is formed.
Lecture 3
Intermolecular forces
Van der Waals forces
Instantly negative part of a molecule interacts
with instantly positive part of another
molecule or induces dipole in another electroneutral molecule. Two dipoles are mutually
stabilising. In macromolecules (polymers) the
force of these electrostatic forces can reach
considerable values. Van der Waals forces have
essential role in the formation of the structure
of biopolymers.
Intermolecular forces
Lecture 3
Van der Waals forces
Energy: 1 - 2 kcal/mole
Intermolecular forces
Lecture 3
Hydrogen bond
Polar molecules: unequal
spatial distribution of the
electrons
Non-polar molecule:
symmetrical spatial
distribution of the
electrons
Lecture 3
Intermolecular forces
Hydrogen bond
H2O
Energy: 3 - 5 kcal/mole
Lecture 3
Intermolecular forces
Hydrogen bond
electrostatic
interaction
between
partially
electronegative atoms (O, N, P) of the polar molecules or
functional groups within molecules and partially
electropositive hydrogen atoms.
R
s+
O H
H sN
R
H
s+
R
O H
sO
R
Intermolecular forces
Lecture 3
Hydrogen bond within the structure of the
biological macromolecules
Complementary interactions of the base
pairs in the nucleic acid structure
Intermolecular forces
Lecture 3
Hydrogen bond within the structure of the
biological macromolecules
a-spiral of the proteins
Intermolecular forces
Hydrogen bond
Lecture 3
Biologically important properties of the water
Surface tension
Lecture 3
Biologically important properties of the water
Cohesion
Lecture 3
Lecture 3
Biologically important properties of the water
High heat capacity
J/kg x oK
cal/g x oC
water
4186
1,0
ice
2090
0,5
aluminum
900
0,22
gold
129
0,03
Biologically important properties of the water
High heat capacity
Lecture 3
Biologically important properties of the water
Cooling through evaporation
Lecture 3
Biologically important properties of the water
Lecture 3
Reduced density at freezing
Biologically important properties of the water
Lecture 3
Reduced density at freezing
Biologically important properties of the water
Lecture 3
Capability to dissolve polar
compounds
Biologically important properties of the water
Lecture 3
Capability to dissolve polar compounds
Polar
compounds
are hydrophilic
The concentration
of the solutions is
measured in
moles per litre
Biologically important properties of the water
Lecture 3
Repulsion of from the surfaces
covered with non-polar compounds
Non-polar
compounds
are
hydrophobic
Intermolecular forces
Lecture 3
Hydrophobic interactions
Many molecules are water-insoluble
(hydrocarbons, fats) or contain hydrophobic
parts (several amino acids). Such molecules tend
to aggregate in the water environment and to
diminish the surface which is exposed to the
water (oil drops in the water).
Minimal surface are which is exposed towards
the water support the energetically favourable
conformation of the hydrophobic (waterinsoluble) molecules.
Lecture 3
Intermolecular forces
Hydrophobic interactions
Micelle of the fatty acids
Energy: 3 - 4 kcal/mole
The dissociation of the water, pH
H2 O
Lecture 3
H+ + OH-
The concentration of
hyrogen (hydronium) and
hydroxide ions is 10-7 M
Only one out of 554 million
water molecules is
dissociated in pure water
The dissociation of the water, pH
H2 O
H+ + OH-
The product of the hydrogen and hydroxide
ion concentrations in solutions is constant
In pure water [H+] · [OH-] = 10 -14 M2
pH = - log [H+]
For pure water pH= -log10-7 = -(-7) = 7
Lecture 3
The dissociation of the water, pH
Lecture 3
pH values of different solutions
1,0
0,9 – 1,8
2,2 – 2,4
Solution
Milk
Saliva
Blood
Vinegar
Sauerkraut,
vine, orange
juice
Black coffee
2,4 – 3,4
4,0 – 4,4
Bile juices
Sea water
pH
6,3 – 6,6
6,5 – 7,5
7,35 –
7,45
7,6 – 8,6
8,0 – 8,5
5,0 – 5,1
Rain water
Urine
5,6 – 6,2
5,5 – 7,5
Ammonia
water
Bleach
0,1 M NaOH
11,0 –
12,0
~12,0
13
Solution
0,1 M HCl
Gastric juice
Lemon juice
pH
Lecture 3
The dissociation of the water, pH
Acids and bases
Acids increase the concentration of
H+ ions in the solution
+
Strong
HCl
H + Cl
Week
H2CO
-
HCO3 + H
-
+
H3PO
H2PO4 + H
H2PO
HPO42-+
H
+
+
Acid
Conjugated base
Strong acids dissociate completely, week acids dissociate
partially
Lecture 3
The dissociation of the water, pH
Acids and bases
Week acids dissociate only partially
-
+
H3PO4
H2PO4 + H
H2PO4
HPO42-+
+
H
pK = the constant of dissociation, the smaller is pK,
the stronger is the acid.
pK numerically identical to pH at which half of the acid
molecules are dissociated.
For two and three-valent acids each step of
dissociation has its own pK.
Lecture 3
The dissociation of the water, pH
Acids and bases
-
Bases increase the OH ion
concentration in the water
+
Strong NaOH
Na + OH
Week
NH3 + H2O
NH4
+
+ OH
-
Lecture 3
The dissociation of the water, pH
Buffer solutions
Solutions of a week acid and conjugated base which
are capable to resist rush changes of pH upon
addition of small amounts of strong acids or bases.
Blood buffer
system
H2CO3
H2CO3
Intracellular
H3PO4
buffer system
H2PO4
-
HCO3 + H
CO2 + H2O
-
HPO4
pK = 6,1
o
+
H2PO4 + H
2-
+
+
+H
(37 C)
pK = 1,8
pK = 7,2
The dissociation of the water, pH
Buffer solutions
Henderson – Haselbach equation:
Lecture 3
The dissociation of the water, pH
Buffer solutions
When small
amount of a
strong acid is
added to the
buffer
solution:
Lecture 3
The dissociation of the water, pH
Lecture 3
If HCl to 0.01 M final concentration is
aded in water final pH will be 2.
If HCl is aded to 0.01 M final concentration
in 0.05 M phosphate buffer solution at pH 7.2
final pH will be :
pH = 7.2 + log 0.67 = 7.2 + (-0.174) = ~ 7.0
The dissociation of the water, pH
Buffer solutions
When small
amount of a
strong base is
added to the
buffer
solution:
Lecture 3
The dissociation of the water, pH
Lecture 3
Buffer solutions
Buffer capacity of the solution is maximal within the
interval of one pH unit around pK point.