chemical bonds, intermolecular forces, properties of water, buffer solutions basic cell biology i...
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CHEMICAL BONDS, INTERMOLECULAR FORCES,
PROPERTIES OF WATER, BUFFER SOLUTIONS
BASIC CELL BIOLOGY
I CHEMISTRY of LIFE
• Covalent bond• Van der Waals forces• Hydrophobic interactions• Hydrogen bond• Biologically important properties of water• pH, acids and bases • Buffer solutions
Lecture 3
CHEMICAL BONDS, INTERMOLECULAR FORCES,
PROPERTIES OF WATER, BUFFER SOLUTIONS
Chemical bond
In forming chemical bonds, atoms donate, acquire, or
share electrons.
Lecture 3
Chemical bond : ionic bondLecture 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 bondLecture 3
Not only the atoms, also functional groups can be ionised through donation or acceptance of the proton.
Ionic bond participates in the formation of the secondary structure of the proteins
Chemical bond : ionic bondLecture 3
Sharing of the pair of electrons through formation of the common
electron shellsOne common pair of the electrons
Formation of the bond
Structural formula
Energy: ~80 kcal/mole
Chemical bond : covalent bondLecture 3
Sharing of the pair of electrons through formation of the common
electron shellsTwo common pairs of the electrons
Formation of the bond
Structural formula
Energy: ~150 kcal/mole
Chemical bond : covalent bondLecture 3
Sharing of the pair of electrons through formation of the common
electron shellsThree common pairs of the electrons
Formation of the bond
Structural formula
Energy: ~200 kcal/mole
Chemical bond : covalent bondLecture 3
Formation of the covalent bond between different atoms: carbon and
hydrogen
Spatial structural formula
Formation of the bond
Structural formula
Chemical bond : covalent bondLecture 3
Structural formula
Carbon atom forms four, oxygen atom forms two common pairs of electrons.
Formation of the covalent bond between different atoms: carbon and
oxygenFormation of the
bond
Chemical bond : covalent bondLecture 3
Structural formula
Nitrogen atom forms three,
hydrogen atom forms one common pairs of electrons.
Formation of the covalent bond between different atoms: carbon and
oxygenFormation of the
bond
Chemical bond : covalent bondLecture 3
Spatial structural formula
Chemical bond : covalent bondLecture 3
Covalent bonds make the backbone of the organic molecules and ensure their stability
Lecture 3Chemical 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.
Intermolecular forces
Van der Waals forcesThe 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 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.
Lecture 3
Intermolecular forcesLecture 3
Energy: 1 - 2 kcal/mole
Van der Waals forces
Hydrogen bond
Polar molecules: unequal spatial
distribution of the electrons
Non-polar molecule:
symmetrical spatial distribution of the
electrons
Intermolecular forcesLecture 3
H2O
Hydrogen bond
Intermolecular forcesLecture 3
Energy: 3 - 5 kcal/mole
Hydrogen bond
Intermolecular forcesLecture 3
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
- + -+
Complementary interactions of the base pairs in the nucleic acid
structure
Hydrogen bond within the structure of the biological macromolecules
Intermolecular forcesLecture 3
Intermolecular forcesLecture 3
Hydrogen bond within the structure of the biological macromolecules
-spiral of the proteins
Hydrogen bond
Intermolecular forcesLecture 3
Surface tension
Biologically important properties of the waterLecture 3
Cohesion
Biologically important properties of the waterLecture 3
High heat capacity
Biologically important properties of the waterLecture 3
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 waterLecture 3
High heat capacity
Cooling through evaporation
Biologically important properties of the waterLecture 3
Reduced density at freezing
Biologically important properties of the waterLecture 3
Reduced density at freezing
Biologically important properties of the waterLecture 3
Capability to dissolve polar compounds
Biologically important properties of the waterLecture 3
Polar compounds
are hydrophilic
The concentration
of the solutions is measured in moles per litre
Capability to dissolve polar compounds
Biologically important properties of the waterLecture 3
Repulsion of from the surfaces covered with non-polar
compounds
Non-polar compounds
are hydrophobi
c
Biologically important properties of the waterLecture 3
Intermolecular forcesLecture 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 (water-insoluble) molecules.
Intermolecular forcesLecture 3
Hydrophobic interactions
Micelle of the fatty acids
Energy: 3 - 4 kcal/mole
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
Lecture 3
The dissociation of the water, pHLecture 3
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
The dissociation of the water, pHLecture 3
Solution pH Solution pH 0,1 M HCl 1,0 Milk 6,3 – 6,6 Gastric juice 0,9 – 1,8 Saliva 6,5 – 7,5 Lemon juice 2,2 – 2,4 Blood 7,35 –
7,45 Vinegar 2,4 – 3,4 Bile juices 7,6 – 8,6 Sauerkraut, vine, orange juice
4,0 – 4,4 Sea water 8,0 – 8,5
Black coffee 5,0 – 5,1 Ammonia water
11,0 – 12,0
Rain water 5,6 – 6,2 Bleach ~12,0 Urine 5,5 – 7,5 0,1 M NaOH 13
pH values of different solutions
Acids and bases
Acids increase the concentration of H+ ions in the solution
Strong HCl H+ + Cl
-
H2CO HCO3- + H
+ H3PO H2PO4
- + H+
Week
H2PO HPO42-+ H
+
Strong acids dissociate completely, week acids dissociate partially
Acid Conjugated base
The dissociation of the water, pHLecture 3
Acids and bases
The dissociation of the water, pHLecture 3
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.
Acids and bases
The dissociation of the water, pHLecture 3
Bases increase the OH- ion
concentration in the water Strong NaOH Na
+ + OH-
Week NH3 + H2O NH4+ + OH
-
Buffer solutions
The dissociation of the water, pHLecture 3
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.
H2CO3 HCO3- + H
+ pK = 6,1 Blood buffer
system H2CO3 CO2 + H2O (37oC)
H3PO4 H2PO4- + H
+ pK = 1,8 Intracellular
buffer system H2PO4
- HPO42- + H
+ pK = 7,2
The dissociation of the water, pHLecture 3
Buffer solutions
Henderson – Haselbach equation:
The dissociation of the water, pHLecture 3
Buffer solutionsWhen small amount of a strong acid is added to the buffer solution:
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, pHLecture 3
The dissociation of the water, pHLecture 3
Buffer solutions
When small amount of a strong base is added to the buffer solution:
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.