Biology 107
Carbon and Molecular Diversity
August 31, 2005
Carbon
Student Objectives: As a result of this lecture and the assigned
reading, you should understand the following:
1.
Role of carbon in life's diversity - next to water, compounds
containing carbon are the most common substances in living
organisms.
2.
The enormous variety of carbon-based molecules is because a
carbon atom has 4 outer shell electrons in a shell that holds 8.
3.
Compounds with the same molecular formula but different
structure are called isomers.
Carbon
4.
The unique properties of an organic compound depend not only
on its carbon skeleton, but also on certain groups of atoms that
are covalently linked to the skeleton. These groups of atoms are
called functional groups, the name reflecting the fact that these
parts of the organic molecules usually are involved in chemical
reactions. See Figure 4.10 in Campbell and Reece.
5.
Most of these functional groups are polar, because their oxygen or
nitrogen atoms are highly electronegative. The polarity tends to
make compounds containing these groups hydrophilic, and
therefore soluble in water - a necessary condition for their roles in
water-based life. Note that many biological molecules have two
or more functional groups (e.g., amino acids - contain at least one
carboxyl as well as one amino group).
Carbon
6.
Organic macromolecules are polymers created through
dehydration synthesis reactions that chemically link the specific
monomers together with covalent bonds. Polymers are broken
down through hydrolysis reactions.
7.
It is the variety in polymers that accounts for the uniqueness of
each organism; the monomers used to make polymers are
essentially universal throughout the biological realm.
Types of Bonds
Intramolecular
Intermolecular
Covalent
Hydrogen
Ionic
Van der Waals
Metallic
Ionic Attractions
Examples of Bond Strengths
Bond Type
Bond Length
(nm)
Bond Strength in
Water (kcal/mole)
Covalent
0.15
90
Ionic
0.25
3
Hydrogen
0.30
1
Van der Waals
(per atom)
0.35
0.1
Organic Molecules Contain Carbon
Valence Shells of Atoms Most Commonly Found in
Organic Molecules
Majors Types of
Isomers
1.
Structural isomers (different
covalent arrangements)
2.
Geometric isomers (differ
around double bond)
3.
Enantiomers (mirror-images
that differ around an
asymmetric, chiral, atom)
What is Chirality?
Immanuel Kant,
1783
“The glove of
one hand
cannot be
used on the
other”
(S)
“sinister”
LEFT
(R)
“rectus”
RIGHT
ENANTIOMERS
Enantiomers have identical physical and chemical properties.
EXCEPT
Ability to rotate the plane of polarized light
and
Rate of reaction and interaction with other chiral compounds
and environments
Importance of Chirality
O
N
H
O
O
N
N
H
O
H
O
N
OH H
(-)-Propranolol
Different activities?
N
O
O
(-)-Thalidomide
H
O
H
(+)-Thalidomide
N
H HO
H
(+)-Propranolol
Same activity different
potency
CHIRALITY AND DRUG
ACTION
Why do enantiomers have the potential for
exhibiting different pharmacodynamic and/or
pharmacokinetic properties?
Primary Functional Groups
Functional Groups
C
O-H
1. Hydroxyl
H
2. Carbonyl
C C O
aldehyde
O
C
C
ketone
C
Functional Groups
3. Carboxyl
O
O H
C C O
C
+
+
H
C O
4. Amino
H
C
N H + H+
H
+
C N H
H
Functional Groups
5. Sulfhydral
C
S-H
6. Phosphate
O H
C O P O
O H
O
C O P O
O
+ 2 H+
Slight Differences in Functional
Groups May Have Dramatic
Functional Effects
Biological Molecules Usually Have More Than One
Functional Group
Dehydration Synthesis Reactions - Additions
Hydrolysis Reaction - Removals
Polymer Synthesis
and Breakdown
Reactions
Synthesis of complex
molecules from simpler
molecules (anabolism) by
dehydration synthesis
reactions
Break down of complex
molecules to simpler
molecules (catabolism) by
hydrolysis reactions
Why so many different metabolic
enzymes in cells?