Biology 107 Carbon and Molecular Diversity

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Biology 107Carbon and Molecular Diversity

• September 1, 2004

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Carbon

• Student Objectives As a result of this lecture
  and the assigned reading, you should understand
  the following
• Role of carbon in life's diversity - next to
  water, compounds containing carbon are the most
  common substances in living organisms.
• The enormous variety of carbon-based molecules is
  because a carbon atom has 4 outer shell electrons
  in a shell that holds 8.
• Compounds with the same molecular formula but
  different structure are called isomers.

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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 Table 4.1 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).

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Carbon

• 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.

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Types of Bonds
Intramolecular Intermolecular
Covalent Hydrogen
Ionic Van der Waals
Metallic Ionic Attractions
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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
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Organic Molecules Contain Carbon
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Valence Shells of Atoms Most Commonly Found in
Organic Molecules
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Majors Types of Isomers

• Structural isomers (different covalent
  arrangements)
• Geometric isomers (differ around double bond)
• Enantiomers (mirror-images that differ around an
  asymmetric, chiral, atom)

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What is Chirality?

• Immanuel Kant,
• 1783
• The glove of one hand cannot be used on the
  other

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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
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Importance of Chirality
Different activities? Same activity
different potency
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CHIRALITY AND DRUG ACTION
Why do enantiomers have the potential for
exhibiting different pharmacodynamic and/or
pharmacokinetic properties?
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Primary Functional Groups

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Primary Functional Groups
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Functional Groups
1. Hydroxyl
2. Carbonyl
aldehyde
ketone
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Functional Groups
3. Carboxyl
H
4. Amino

H
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Functional Groups
5. Sulfhydral
6. Phosphate
2 H
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Slight Differences in Functional Groups May Have
Dramatic Functional Effects
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Biological Molecules Usually Have More Than One
Functional Group
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Dehydration Synthesis Reactions - Additions
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Hydrolysis Reaction - Removals
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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?