Biology 107 Carbon and Molecular Diversity September 1, 2004.

Biology 107Biology 107

Carbon and Molecular DiversityCarbon and Molecular Diversity

September 1, 2004September 1, 2004

CarbonCarbonStudent Objectives:Student Objectives: As a result of this lecture and the assigned reading, you should As a result of this lecture and the assigned reading, you should

understand the following:understand the following:

1.1. Role of carbon in life's diversity - next to water, compounds containing carbon are the Role of carbon in life's diversity - next to water, compounds containing carbon are the most common substances in living organisms.most common substances in living organisms.

2.2. The enormous variety of carbon-based molecules is because a carbon atom has 4 outer The enormous variety of carbon-based molecules is because a carbon atom has 4 outer shell electrons in a shell that holds 8.shell electrons in a shell that holds 8.

3.3. Compounds with the same molecular formula but different structure are calledCompounds with the same molecular formula but different structure are called isomers isomers..

CarbonCarbon4.4. The unique properties of an organic compound depend not only The unique properties of an organic compound depend not only

on its carbon skeleton, but also on certain groups of atoms that on its carbon skeleton, but also on certain groups of atoms that are covalently linked to the skeleton. These groups of atoms are are covalently linked to the skeleton. These groups of atoms are called functional groups, the name reflecting the fact that these called functional groups, the name reflecting the fact that these parts of the organic molecules usually are involved in chemical parts of the organic molecules usually are involved in chemical reactions. See Table 4.1 in Campbell and Reece.reactions. See Table 4.1 in Campbell and Reece.

5.5. Most of these functional groups are polar, because their oxygen Most of these functional groups are polar, because their oxygen or nitrogen atoms are highly electronegative. The polarity tends or nitrogen atoms are highly electronegative. The polarity tends to make compounds containing these groups hydrophilic, and to make compounds containing these groups hydrophilic, and therefore soluble in water - a necessary condition for their roles in therefore soluble in water - a necessary condition for their roles in water-based life. Note that many biological molecules have two water-based life. Note that many biological molecules have two or more functional groups (e.g., amino acids - contain at least one or more functional groups (e.g., amino acids - contain at least one carboxyl as well as one amino group).carboxyl as well as one amino group).

CarbonCarbon

6.6. Organic macromolecules are polymers created through Organic macromolecules are polymers created through dehydration synthesis reactionsdehydration synthesis reactions that chemically link the specific that chemically link the specific monomers together with covalent bonds. Polymers are broken monomers together with covalent bonds. Polymers are broken down through down through hydrolysis reactionshydrolysis reactions..

7.7. It is the variety in polymers that accounts for the uniqueness of It is the variety in polymers that accounts for the uniqueness of each organism; the monomers used to make polymers are each organism; the monomers used to make polymers are essentially universal throughout the biological realm. essentially universal throughout the biological realm.

Types of BondsTypes of BondsIntramolecularIntramolecular IntermolecularIntermolecular

CovalentCovalent HydrogenHydrogen

IonicIonic Van der WaalsVan der Waals

MetallicMetallic Ionic AttractionsIonic Attractions

Examples of Bond StrengthsExamples of Bond Strengths

Bond TypeBond Type Bond Length Bond Length (nm)(nm)

Bond Strength in Bond Strength in Water (kcal/mole)Water (kcal/mole)

CovalentCovalent 0.150.15 9090

IonicIonic 0.250.25 33

HydrogenHydrogen 0.300.30 11

Van der Waals Van der Waals (per atom)(per atom)

0.350.35 0.10.1

Organic Molecules Contain CarbonOrganic Molecules Contain Carbon

Valence Shells of Atoms Most Commonly Found in Valence Shells of Atoms Most Commonly Found in Organic MoleculesOrganic Molecules

Majors Types of Majors Types of IsomersIsomers

1.1. Structural isomers (different Structural isomers (different covalent arrangements)covalent arrangements)

2.2. Geometric isomers (differ Geometric isomers (differ around double bond)around double bond)

3.3. Enantiomers (mirror-images Enantiomers (mirror-images that differ around an that differ around an asymmetric, chiral, atom)asymmetric, chiral, atom)

What is Chirality?Immanuel Kant, Immanuel Kant,

17831783

““The glove of one hand The glove of one hand cannot be used on the cannot be used on the other”other”

(R)(R)““rectus” rectus” RIGHTRIGHT

(S)(S)““sinister”sinister” LEFTLEFT

ENANTIOMERS

Enantiomers have identical physical and chemical properties.

EXCEPT

Ability to rotate the plane of polarized lightAbility to rotate the plane of polarized light

and

Rate of reaction and interaction with other chiral compounds Rate of reaction and interaction with other chiral compounds and environmentsand environments

Importance of ChiralityImportance of Chirality

N

N

O

OO

O

H

H N

O

O

H

N

O

O

H

(-)-Thalidomide (+)-Thalidomide

NHOHH

N

HH OH

(-)-Propranolol (+)-Propranolol

Different activities?Different activities?

Same activity different Same activity different potencypotency

CHIRALITY AND DRUG CHIRALITY AND DRUG ACTIONACTION

Why do enantiomers have the potential for exhibiting different pharmacodynamic and/or pharmacokinetic properties?

Primary Functional Groups

Primary Functional Groups

C O-H

Functional GroupsFunctional Groups

1. Hydroxyl

C C O

H 2. Carbonyl

C C C

O

aldehyde ketone

C O

O H

C C OO-

C

3. Carboxyl

Functional GroupsFunctional Groups

C N

H

H N

H

H

H

C+ H+

+ H+

4. Amino

+

P

O H

O H

OOC PO-

O-

OOC

+ 2 H+

6. Phosphate

Functional GroupsFunctional Groups

5. Sulfhydral C S-H

Slight Differences in Functional Slight Differences in Functional Groups May Have Dramatic Groups May Have Dramatic

Functional EffectsFunctional Effects

Biological Molecules Usually Have More Than One Biological Molecules Usually Have More Than One Functional GroupFunctional Group

Dehydration Synthesis Reactions - Additions

Hydrolysis Reaction - RemovalsHydrolysis Reaction - Removals

Polymer Synthesis Polymer Synthesis and Breakdown and Breakdown

ReactionsReactions

Synthesis of complex Synthesis of complex molecules from simpler molecules from simpler molecules (molecules (anabolismanabolism) by ) by dehydration synthesis dehydration synthesis reactionsreactions

Break down of complex Break down of complex molecules to simpler molecules to simpler molecules (molecules (catabolismcatabolism) by ) by hydrolysis reactionshydrolysis reactions

Why so many different metabolic Why so many different metabolic enzymes in cells?enzymes in cells?