From Atoms to Biological Molecules

Periodical Table
Life prefers lighter atoms
(1) More abundant on Earth (2) Stronger bonding between small atoms

Chemical properties
H CNO

The atomic composition of living organism is more complex than others Atomic sizes

1H
1s Electrons on the outer shell

6C

7N 8O
2s 2p

sp3

O
sp3
The tetrahedral structure of carbon orbital has rigid steric strain which makes the basic building unit of protein conformation

Components of the early atmosphere

H2

CH4 NH3 H2O

Components of the early atmosphere

H2 C-C

CH4 NH3 H2O

Review the structure of water

Organic compound
Electronegativity

C
CH3

COOH NH2

- +
lp

-d

lp

O 3.5
N 3.0 C 2.5 H 2.1

O
+d
Permanent dipole

Functional group
If atoms in a functional group have notable difference in electronegativity, then this functional group will express high polarity and will be highly active

High polarity High dielectric constant H-bond formation pH influence

Exaggerated Model for Water Molecule

-d -d

-d
-d
+d +d

lp lp

sp3
H
+d

H
+d

O
H O H3C O H5C2 H H H

Dielectric Constant
Water Methanol Ethanol Ammonia Acetic acid Chloroform Ethyl ether Benzene Carbon tetrachloride 80.4 33.6 24.3 17.3 6.15 4.81 4.43 2.28 2.24

O H5C2 C2H5

ClCCl
Cl

Cl
ClCCl Cl

Molecules with asymmetrical distribution of electronegativity have higher polarity

Ionic Bond Is Not Stable in Water Solution

Solvation
+

+ + O + C - + O + +

- -+ +- + -+ + + - - + - -+ + - -+ + - -+ + - -+ -+ + - +

+?-

- + -

H H N +H

But enzyme forms stable binding with its substrate in water

Bond Energy in Water Might Be Different

Bond length In vacuum Water solution Covalent bond Ionic bond 0.15 nm 0.25 nm 0.30 nm 0.35 nm 90 80 90 3 1 0.1 kcal/mole

Hydrogen bond
Van der Waal force

4
0.1

Hydrogen Bond (H-Bond)

The linearity is important for a perfect H-bond

H
Weaker H-bond

Affinity between Two Molecules

Like Dissolves Like

Molecules having similar polarity will attract each other

Polar Polar
Nonpolar Nonpolar

Energy of Chemical Bonds in Cells

Adapted from Alberts et al (2002) Molecular Biology of the Cell (4e) p.53

Room Temperature

ATP Hydrolysis Covalent bond Glucose Oxidation

0.1

10

100 kcal/mole

Secondary bond
Van der Waal force Hydrophobic bond Hydrogen bond Ionic bond Covalent bond
0.1 kcal/mole

1 kcal/mole
1 kcal/mole 3 kcal/mole 90 kcal/mole

Secondary Bonds Contribute to Molecular Affinity

Reversible non-covalent binding