CHEMICAL BONDS, INTERMOLECULAR FORCES, PROPERTIES OF WATER, BUFFER SOLUTIONS BASIC CELL BIOLOGY I...

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.


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


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


electron shellsTwo common pairs of the electrons


Structural formula




electron shellsThree common pairs of the electrons


Structural formula



Formation of the covalent bond between different atoms: carbon and

hydrogen

Spatial structural formula


Structural formula


Structural formula

Carbon atom forms four, oxygen atom forms two common pairs of electrons.


oxygenFormation of the

bond


Structural formula

Nitrogen atom forms three,

hydrogen atom forms one common pairs of electrons.


oxygenFormation of the

bond


Spatial structural formula


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


H2O

Hydrogen bond



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

- + -+

Complementary interactions of the base pairs in the nucleic acid

structure

Hydrogen bond within the structure of the biological macromolecules



Hydrogen bond within the structure of the biological macromolecules

-spiral of the proteins

Hydrogen bond


Surface tension

Biologically important properties of the waterLecture 3

Cohesion


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


High heat capacity

Cooling through evaporation


Reduced density at freezing


Capability to dissolve polar compounds


Polar compounds

are hydrophilic

The concentration

of the solutions is measured in moles per litre

Capability to dissolve polar compounds


Repulsion of from the surfaces covered with non-polar

compounds

Non-polar compounds

are hydrophobi

c



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.


Hydrophobic interactions

Micelle of the fatty acids


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


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


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.

Acids and bases


Bases increase the OH- ion

concentration in the water Strong NaOH Na

+ + OH-

Week NH3 + H2O NH4+ + OH

-

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.

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


Buffer solutions

Henderson – Haselbach equation:


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



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.

CHEMICAL BONDS, INTERMOLECULAR FORCES, PROPERTIES OF WATER, BUFFER SOLUTIONS BASIC CELL BIOLOGY I...

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