From Atoms to Biological Molecules
Chemical properties
Periodical Table
H
CNO
Life prefers lighter atoms
Atomic
sizes
(1) More abundant on Earth
(2) Stronger bonding between small atoms
1H
6C
1s
Electrons on
the outer shell
H
The atomic composition
of living organism is more
complex than others
7N 8O
2s 2p
C
N
O
sp3
Components of the early
atmosphere
H2
sp3
CH4 NH3 H2O
The tetrahedral structure
of carbon orbital has rigid
steric strain which makes
the basic building unit of
protein conformation
Juang RH (2004) BCbasics
Components of the early
atmosphere
H2
CH4 NH3 H2O
Review the structure of water
C-C
- +
Organic compound
Electronegativity
O 3.5
N 3.0
C 2.5
H 2.1
C
R
COOH
C
lp
-d
lp
NH2
CH3
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
O
+d
Permanent
dipole
● High polarity
● High dielectric constant
● H-bond formation
● pH influence
Juang RH (2004) BCbasics
Exaggerated Model for Water Molecule
-d
-d
-d
-d
+d
+
+d
-
lp
sp3
lp
H
+d
H
+d
Adapted from Zubay (1988) Biochemistry (2e) p.57
O
H
H
O
H3 C
H
O
H5C2
H
O
H5C2
C2H5
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
H
Cl–C–Cl
Cl
Cl
Cl–C–Cl
Molecules with asymmetrical distribution
of electronegativity have higher polarity
Cl
Adapted from Bohinski (1987) Modern Concepts in Biochemistry (5e) p.37
Solvation
+
-
+
+
-+ + + - - - + + + +
+
+
+
- + - +
-+ + - -+ + -
+
+
O +
C - +
O +
+
-
-
-
H
H N
+H
- -
+?-
● But enzyme forms stable binding with its substrate in water
+
-
Adapted from Alberts et al (2002) Molecular Biology of the Cell (4e) p.115
Adapted from Nelson & Cox (2000) Lehninger Principles of Biochemistry (3e) p.87
Ionic Bond Is Not Stable in Water Solution
Bond Energy in Water Might Be Different
Bond length In vacuum Water solution
Covalent bond
0.15 nm
90
90
Ionic bond
0.25 nm
80
3
Hydrogen bond
0.30 nm
4
1
Van der Waal force
0.35 nm
0.1
0.1
kcal/mole
Adapted from Alberts et al (2002) Molecular Biology of the Cell (4e) p.57
Hydrogen Bond (H-Bond)
The linearity is important for a perfect H-bond
+
N
H
Weaker H-bond
O
O
Adapted from Alberts et al (2002) Molecular Biology of the Cell (4e) p.58
Affinity between Two Molecules
Like
Dissolves
Like
Molecules having similar polarity will attract each other
Polar → Polar
Nonpolar → Nonpolar
Juang RH (2004) BCbasics
Energy of Chemical Bonds in Cells
Adapted from Alberts et al (2002) Molecular Biology of the Cell (4e) p.53
Room Temperature
0.1
ATP Hydrolysis Covalent bond Glucose Oxidation
1
10
Secondary bond
Van der Waal force
0.1 kcal/mole
Hydrophobic bond
1 kcal/mole
Hydrogen bond
1 kcal/mole
Ionic bond
Covalent bond
100
kcal/mole
3 kcal/mole
90 kcal/mole
Juang RH (2004) BCbasics
Secondary Bonds Contribute to Molecular Affinity
x
Reversible non-covalent binding
Adapted from Alberts et al (2002) Molecular Biology of the Cell (4e) p.161