CHEMICAL BONDS, INTERMOLECULAR FORCES, PROPERTIES OF WATER, BUFFER SOLUTIONS

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BASIC CELL BIOLOGY
I CHEMISTRY of LIFE
CHEMICAL BONDS, INTERMOLECULAR FORCES, PROPERTIES
OF WATER, BUFFER SOLUTIONS
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Lecture 3
CHEMICAL BONDS, INTERMOLECULAR FORCES, PROPERTIES
OF WATER, BUFFER SOLUTIONS

• Covalent bond
• Van der Waals forces
• Hydrophobic interactions
• Hydrogen bond
• Biologically important properties of water
• pH, acids and bases
• Buffer solutions

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Lecture 3
Chemical bond
In forming chemical bonds, atoms donate, acquire,
or share electrons.
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Lecture 3
Chemical bond ionic bond
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.
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Lecture 3
Chemical bond ionic bond
Not only the atoms, also functional groups can be
ionised through donation or acceptance of the
proton.
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Lecture 3
Chemical bond ionic bond
Ionic bond participates in the formation of the
secondary structure of the proteins
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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
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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
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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
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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
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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
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Lecture 3
Chemical bond covalent bond
Formation of the covalent bond between different
atoms carbon and oxygen
Structural formula
Formation of the bond
Nitrogen atom forms three, hydrogen atom forms
one common pairs of electrons.
Spatial structural formula
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Lecture 3
Chemical bond covalent bond
Covalent bonds make the backbone of the organic
molecules and ensure their stability
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Lecture 3
Chemical bonds
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.
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Lecture 3
Intermolecular forces
Van der Waals forces 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.
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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
electro-neutral 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.
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Lecture 3
Intermolecular forces
Van der Waals forces
Energy 1 - 2 kcal/mole
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Lecture 3
Intermolecular forces
Hydrogen bond
Polar molecules unequal spatial distribution of
the electrons
Non-polar molecule symmetrical spatial
distribution of the electrons
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Lecture 3
Intermolecular forces
Hydrogen bond
H2O
Energy 3 - 5 kcal/mole
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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.
H R O H N R H
R O H O R
s-
s
s-
s
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Lecture 3
Intermolecular forces
Hydrogen bond within the structure of the
biological macromolecules
Complementary interactions of the base pairs in
the nucleic acid structure
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Lecture 3
Intermolecular forces
Hydrogen bond within the structure of the
biological macromolecules
a-spiral of the proteins
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Lecture 3
Intermolecular forces
Hydrogen bond
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Lecture 3
Biologically important properties of the water
Surface tension
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Lecture 3
Biologically important properties of the water
Cohesion
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Lecture 3
Biologically important properties of the water
High heat capacity
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Lecture 3
Biologically important properties of the water
High heat capacity
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Lecture 3
Biologically important properties of the water
Cooling through evaporation
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Lecture 3
Biologically important properties of the water
Reduced density at freezing
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Lecture 3
Biologically important properties of the water
Reduced density at freezing
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Lecture 3
Biologically important properties of the water
Capability to dissolve polar compounds
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Lecture 3
Biologically important properties of the water
Capability to dissolve polar compounds
Polar compounds are hydrophilic
The concentration of the solutions is measured in
moles per litre
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Lecture 3
Biologically important properties of the water
Repulsion of from the surfaces covered with
non-polar compounds
Non-polar compounds are hydrophobic
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Lecture 3
Intermolecular forces
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
(water-insoluble) molecules.
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Lecture 3
Intermolecular forces
Hydrophobic interactions
Micelle of the fatty acids
Energy 3 - 4 kcal/mole
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Lecture 3
The dissociation of the water, pH
H2O 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
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Lecture 3
The dissociation of the water, pH
H2O 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
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Lecture 3
The dissociation of the water, pH
pH values of different solutions
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Lecture 3
The dissociation of the water, pH
Acids and bases
Acid
Conjugated base
Strong acids dissociate completely, week acids
dissociate partially
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Lecture 3
The dissociation of the water, pH
Acids and bases
Week acids dissociate only partially
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.
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Lecture 3
The dissociation of the water, pH
Acids and bases
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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.
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Lecture 3
The dissociation of the water, pH
Buffer solutions
Henderson Haselbach equation
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Lecture 3
The dissociation of the water, pH
Buffer solutions
When small amount of a strong acid is added to
the buffer solution
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Lecture 3
The dissociation of the water, pH
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
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Lecture 3
The dissociation of the water, pH
Buffer solutions
When small amount of a strong base is added to
the buffer solution
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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.