sp

3
Components of the early
atmosphere
H
2
CH
4
NH
3
H
2
O
Life prefers lighter atoms
(1) More abundant on Earth
(2) Stronger bonding between small atoms
From Atoms to Biological Molecules
Chemical properties
Atomic
sizes
The atomic composition
of living organism is more
complex than others
The tetrahedral structure
of carbon orbital has rigid
steric strain which makes
the basic building unit of
protein conformation
Electrons on
the outer shell
Periodical Table
H C N O
1
H
6
C
7
N
8
O
sp
3
1s 2s 2p
H
C N O
Juang RH (2004) BCbasics
Review the structure of water
Permanent
dipole
Electro-
negativity
O 3.5
N 3.0
C 2.5
H 2.1
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
C-C
+d
-d
Organic compound
Functional group
O
lp lp
Components of the early
atmosphere
H
2
CH
4
NH
3
H
2
O
C
C
CH
3
COOH

R

NH
2
- +
Juang RH (2004) BCbasics
H
Exaggerated Model for Water Molecule
Adapted from Zubay (1988) Biochemistry (2e) p.57
-
+
H
+d
+d
-d
-d
-d -d
+d +d
sp
3
lp
lp
Water 80.4
Methanol 33.6
Ethanol 24.3
Ammonia 17.3
Acetic acid 6.15
Chloroform 4.81
Ethyl ether 4.43
Benzene 2.28
Carbon tetrachloride 2.24
Dielectric Constant
Adapted from Bohinski (1987) Modern Concepts in Biochemistry (5e) p.37
Cl
ClCCl
Cl
H
ClCCl
Cl
C
2
H
5
H
5
C
2
O
H H

O
H
3
C

O
H
H
5
C
2
O
H
Molecules with asymmetrical distribution
of electronegativity have higher polarity
Ionic Bond Is Not Stable in Water Solution
A
d
a
p
t
e
d

f
r
o
m

A
l
b
e
r
t
s

e
t

a
l

(
2
0
0
2
)

M
o
l
e
c
u
l
a
r

B
i
o
l
o
g
y

o
f

t
h
e

C
e
l
l

(
4
e
)

p
.
1
1
5

-
+
+ - ?
C
O
O
N H
H
H
+
-
+
+
+
+
+
-
-
-
-
-
-
+
-
-
-
-
-
+
-
+ + -
+
-
+
-
+
-
+
-
+
-
+
+
+
+
+
-
-
+
-
-
-
+
+
- +
-
+
+
A
d
a
p
t
e
d

f
r
o
m

N
e
l
s
o
n

&

C
o
x

(
2
0
0
0
)

L
e
h
n
i
n
g
e
r

P
r
i
n
c
i
p
l
e
s

o
f

B
i
o
c
h
e
m
i
s
t
r
y

(
3
e
)

p
.
8
7

Solvation
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
Hydrogen bond
Van der Waal force
0.15 nm
0.25 nm
0.30 nm
0.35 nm
90
80
4
0.1
90
3
1
0.1
kcal/mole
Adapted from Alberts et al (2002) Molecular Biology of the Cell (4e) p.57
N
H
O
+
Hydrogen Bond (H-Bond)
The linearity is important for a perfect H-bond
O
Weaker H-bond
Adapted from Alberts et al (2002) Molecular Biology of the Cell (4e) p.58
Polar Polar
Nonpolar Nonpolar
Like
Dissolves
Like
Affinity between Two Molecules
Juang RH (2004) BCbasics
Molecules having similar polarity will attract each other
Energy of Chemical Bonds in Cells
0.1 1 10 100
kcal/mole
Room Temperature
Secondary bond
ATP Hydrolysis Covalent bond Glucose Oxidation
Hydrogen bond
Ionic bond
Hydrophobic bond
90 kcal/mole
3 kcal/mole
1 kcal/mole
1 kcal/mole
0.1 kcal/mole
Covalent bond
Van der Waal force
Adapted from Alberts et al (2002) Molecular Biology of the Cell (4e) p.53
Juang RH (2004) BCbasics
Secondary Bonds Contribute to Molecular Affinity
Adapted from Alberts et al (2002) Molecular Biology of the Cell (4e) p.161
Reversible non-covalent binding
x