Cell04 Chemistry

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From Atoms to Biological Molecules

Chemical properties The atomic composition


Periodical Table of living organism is more
H
CNO complex than others
Life prefers lighter atoms
Atomic
(1) More abundant on Earth sizes
(2) Stronger bonding between small atoms

1
H 6
C N
7
O
8
sp3
1s 2s 2p
Electrons on
the outer shell H C N O
The tetrahedral structure
sp3 of carbon orbital has rigid
steric strain which makes
Components of the early the basic building unit of
atmosphere H2 CH4 NH3 H2O protein conformation

Juang RH (2004) BCbasics


Components of the early
atmosphere H2 CH4 NH3 H2O
Review the structure of water
C-C
Organic compound - +
COOH
lp - lp
C
Electro-
C
NH2
negativity
R CH3 O
O 3.5
N 3.0 Functional group Permanent
+ dipole
C 2.5 If atoms in a functional group
have notable difference in ● High polarity
H 2.1 electronegativity, then this ● High dielectric constant
functional group will express ● H-bond formation
high polarity and will be ● pH influence
highly active

Juang RH (2004) BCbasics


Exaggerated Model for Water Molecule
- -

-

-
lp
+ +
lp
sp 3

+ H
- +
H
+
Adapted from Zubay (1988) Biochemistry (2e) p.57
O
H H Dielectric Constant
O Water 80.4
H3C H Methanol 33.6
O
Ethanol 24.3
H5C2 H
Ammonia 17.3
Acetic acid 6.15 H

O Chloroform 4.81 Cl–C–Cl


H5C2 C2H5 Ethyl ether 4.43 Cl
Benzene 2.28
Cl
Carbon tetrachloride 2.24
Cl–C–Cl
Molecules with asymmetrical distribution
Cl
of electronegativity have higher polarity
Adapted from Bohinski (1987) Modern Concepts in Biochemistry (5e) p.37
Ionic Bond Is Not Stable in Water Solution
Adapted from Nelson & Cox (2000) Lehninger Principles of Biochemistry (3e) p.87

+ + -
-
Solvation
H
O +

Adapted from Alberts et al (2002) Molecular Biology of the Cell (4e) p.115
+
-
C - + - H N
+H
O + - -
-
+
+
+?-
- + - -
-
- + -- + -
+
+
+ +

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

● 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 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 O
Weaker H-bond
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 ATP Hydrolysis Covalent bond Glucose Oxidation

0.1 1 10 100

Secondary bond kcal/mole

Van der Waal force 0.1 kcal/mole

Hydrophobic bond 1 kcal/mole

Hydrogen bond 1 kcal/mole

Ionic bond 3 kcal/mole

Covalent bond 90 kcal/mole

Juang RH (2004) BCbasics


Secondary Bonds Contribute to Molecular Affinity

Reversible non-covalent binding


Adapted from Alberts et al (2002) Molecular Biology of the Cell (4e) p.161

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