A. Organic chemistry is the study of carbon compounds




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CHAPTER 4

CARBON AND

MOLECULAR DIVERSITY

OUTLINE

I. The Importance of Carbon

A. Organic chemistry is the study of carbon compounds

B. Carbon atoms are the most versatile building blocks of molecules

C. Variation in carbon skeletons contributes to the diversity of organic molecules

II. Functional Groups

A. Functional groups also contribute to the molecular diversity of life

OBJECTIVES

After reading this chapter and attending lecture, the student should be able to:

1. Summarize the philosophies of vitalism and mechanism, and explain how they

influenced the development of organic chemistry, as well as mainstream biological

thought.

2. Explain how carbonÕs electron configuration determines the kinds and number of bonds

carbon will form.

3. Describe how carbon skeletons may vary, and explain how this variation contributes to

the diversity and complexity of organic molecules.

4. Distinguish among the three types of isomers: structural, geometric and enantiomers.

5. Recognize the major functional groups, and describe the chemical properties of organic

molecules in which they occur.

KEY TERMS

organic chemistry enantiomer aldehyde amine

hydrocarbon functional group ketone sulfhydryl group

isomer hydroxyl group carboxyl group thiol

structural isomer alcohol carboxylic acid phosphate group

geometric isomer carbonyl group amino group

LECTURE NOTES

Aside from water, most biologically important molecules are carbon-based (organic).

The structural and functional diversity of organic molecules emerges from the ability of carbon

to form large, complex and diverse molecules by bonding to itself and to other elements such as

H, O, N, S, and P.

34 Unit I The Chemistry of Life

I. The Importance of Carbon

A. Organic chemistry is the study of carbon compounds

Organic chemistry = The branch of chemistry that specializes in the study of carbon

compounds.

Organic molecules = Molecules that contain carbon

Vitalism = Belief in a life force outside the jurisdiction of chemical/physical laws.

á Early 19th century organic chemistry was built on a foundation of vitalism

because organic chemists could not artificially synthesize organic compounds. It

was believed that only living organisms could produce organic compounds.

Mechanism = Belief that all natural phenomena are governed by physical and chemical

laws.

¥ Pioneers of organic chemistry began to synthesize organic compounds from

inorganic molecules. This helped shift mainstream biological thought from

vitalism to mechanism.

¥ For example, Friedrich Wohler synthesized urea in 1828; Hermann Kolbe

synthesized acetic acid.

¥ Stanley Miller (1953) demonstrated the possibility that organic compounds

could have been produced under the chemical conditions of primordial Earth.

B. Carbon atoms are the most versatile building blocks of molecules

The carbon atom:

¥ Usually has an atomic number of 6; therefore, it has 4 valence electrons.

¥ Usually completes its outer energy shell by sharing valence electrons in four

covalent bonds. (Not likely to form ionic bonds.)

Emergent properties, such as the kinds and number of bonds carbon will form, are

determined by their tetravalent electron configuration.

¥ It makes large, complex molecules possible. The carbon atom is a central point

from which the molecule branches off into four directions.

¥ It gives carbon covalent compatibility with many different elements. The four

major atomic components of organic molecules are as follows:

¥ It determines an organic moleculeÕs three-dimensional shape, which may affect

molecular function. For example, when carbon forms four single covalent

bonds, the four valence orbitals hybridize into teardrop-shaped orbitals that

angle from the carbon atoms toward the corners of an imaginary tetrahedron.

Students have problems visualizing shapes of organic molecules in three dimensions.

Specific examples can be enhanced by an overhead transparency of ball-and-stick or

space-filling models. A large three-dimensional molecular model that can be held up

in front of class works best (see Campbell, Figure 4.2)

Chapter 4 Carbon and Molecular Diversity 35

C. Variation in carbon skeletons contributes to the diversity of organic

molecules

Covalent bonds link carbon atoms together in long chains that form the skeletal

framework for organic molecules. These carbon skeletons may vary in:

¥ Length

¥ Shape (straight chain, branched, ring)

¥ Number and location of double bonds

¥ Other elements covalently bonded to available sites

This variation in carbon skeletons contributes to the complexity and diversity of

organic molecules (see Campbell, Figure 4.4).

Hydrocarbons = Molecules containing only carbon and hydrogen

¥ Are major components of fossil fuels produced from the organic remains of

organisms living millions of years ago, though they are not prevalent in living

organisms.

¥ Have a diversity of carbon skeletons which produce molecules of various

lengths and shapes.

¥ As in hydrocarbons, a carbon skeleton is the framework for the large diverse

organic molecules found in living organisms. Also, some biologically important

molecules may have regions consisting of hydrocarbon chains (e.g. fats).

¥ Hydrocarbon chains are hydrophobic because the C-C and C-H bonds are

nonpolar.

1. Isomers

Isomers = Compounds with the same molecular formula but with different structures

and hence different properties. Isomers are a source of variation among organic

molecules.

There are three types of isomers (see Campbell, Figure 4.6):

Structural isomers = Isomers that differ in the covalent arrangement of their

atoms.

H

|

H-C-H

H H H H H H

| | | | | |

H-C-C-C-C-H H-C-C-C-H

| | | | | | |

H H H H H H H

¥ Number of possible isomers increases as the carbon skeleton size

increases.

¥ May also differ in the location of double bonds.

Geometric isomers = Isomers which share the same covalent partnerships, but

differ in their spatial arrangements.

HO OH H OH

\ / \ /

C = C C = C

/ \ / \

H H HO H

¥ Result from the fact that double bonds will not allow the atoms they

join to rotate freely about the axis of the bonds.

¥ Subtle differences between isomers affects their biological activity.

36 Unit I The Chemistry of Life

Enantiomers = Isomers that are mirror images of each other.

¥ Can occur when four different atoms or groups of atoms are bonded to

the same carbon (asymmetric carbon).

¥ There are two different spatial arrangements of the four groups around

the asymmetric carbon. These arrangements are mirror images.

¥ Usually one form is biologically active and its mirror image is not.

It is often helpful to point at the pharmacological significance of

enantiomers, e.g., Campbell, Figure 4.7.

II. Functional Groups

A. Functional groups also contribute to the molecular diversity of life

Small characteristic groups of atoms (functional groups) are frequently bonded to the

carbon skeleton of organic molecules. These functional groups:

¥ Have specific chemical and physical properties.

¥ Are the regions of organic molecules which are commonly chemically reactive.

¥ Behave consistently from one organic molecule to another.

¥ Depending upon their number and arrangement, determine unique chemical

properties of organic molecules in which they occur.

As with hydrocarbons, diverse organic molecules found in living organisms have carbon

skeletons. In fact, these molecules can be viewed as hydrocarbon derivatives with

functional groups in place of H, bonded to carbon at various sites along the molecule.

1. The hydroxyl group

Hydroxyl group = A functional group that consists of a hydrogen atom bonded to

an oxygen atom, which in turn is bonded to carbon (-OH).

á Is a polar group; the bond between the oxygen and hydrogen is a polar

covalent bond.

á Makes the molecule to which it is attached water soluble. Polar water

molecules are attracted to the polar hydroxyl group which can form

hydrogen bonds.

á Organic compounds with hydroxyl groups are called alcohols.

2. The carbonyl group

Carbonyl group = Functional group that consists of a carbon atom double-bonded

to oxygen (-CO).

¥ Is a polar group. The oxygen can be involved in hydrogen bonding, and

molecules with his functional group are water soluble.

¥ Is a functional group found in sugars.

l-isomer d-isomer

Chapter 4 Carbon and Molecular Diversity 37

¥ If the carbonyl is at the end off the carbon skeleton, the compound is an

aldehyde.

OH OH O

| | //

H-C 3/4 C 3/4 C

| | |

H H H

Glyceraldehyde

¥ If the carbonyl is at the end of the carbon skeleton, the compound is a

ketone.

H O H

|  |

H-C 3/4 C 3/4 C-H

| |

H H

Acetone

3. The carboxyl group

Carboxyl group = Functional group that consists of a carbon atom which is both

double-bonded to an oxygen and single-bonded to the oxygen of a hydroxyl group

(-COOH).

¥ Is a polar group and water soluble. The covalent bond between oxygen and

hydrogen is so polar, that the hydrogen reversibly dissociates as H+. This

polarity results from the combined effect of the two electronegative

oxygen atoms bonded to the same carbon.

H O H O

| // | //

H-C-C H-C-C + H+

| \ | \

H OH H OAcetic

Acetate Hydrogen

acid ion ion

¥ Since it donates protons, this group has acidic properties. Compounds with

this functional group are called carboxylic acids.

4. The amino group

Amino group = Functional group that consists of a nitrogen atom bonded to two

hydrogens and to the carbon skeleton (-NH2).

¥ Is a polar group and soluble in water.

¥ Acts as a weak base. The unshared pair of electrons on the nitrogen can

accept a proton, giving the amino group a +1 charge.

H H

/ /

R-N + H+ R-+N-H

\ \

H H

Amine Ammonium

ion

¥ Organic compounds with this function group are called amines.

5. The Sulfhydryl group

Sulfhydryl group = Functional group which consists of an atom of sulfur bonded to

an atom of hydrogen (-SH).

38 Unit I The Chemistry of Life

¥ Help stabilize the structure of proteins. (Disulfide bridges will be discussed

with tertiary structure of proteins in Chapter 5, Structure and Function of

Macromolecules.)

¥ Organic compounds with this functional group are called thiols.

6. The phosphate group

Phosphate group = Functional group which is the dissociated form of phosphoric

acid (H3PO4).

¥ Loss of two protons by dissociation leaves the phosphate group with a

negative charge.

O O

1/21/2 1/21/2

R-O-P-OH R-O-P-O- + 2H+

| |

OH O-

¥ Has acid properties since it loses protons.

¥ Polar group and soluble in water.

¥ Organic phosphates are important in cellular energy storage and transfer.

(ATP is discussed with energy for cellular work in Chapter 6: Introduction

to Metabolism.)

In lecture, you may also choose to include the methyl group (-CH3) as an

example of a nonpolar hydrophobic functional group. This is helpful later in the

course in explaining how nonpolar amino acids contribute to the tertiary structure

of proteins including integral membrane proteins.

To impress upon students how important functional groups are in determining

chemical behavior of organic molecules, use the following demonstration: show a

comparison of estradiol and testosterone and ask students to find the differences in

functional groups. Ask one male and female student to stand up or show pictures of

sexual dimorphism in other vertebrates. Point out that differences between males

and females are due to slight variation in functional groups attached to sex

hormones.

REFERENCES

Campbell, N. et al. Biology. 5th ed. Menlo Park, California: Benjamin/Cummings, 1998.

Lehninger, A.L., D.L. Nelson and M.M. Cox. Principles of Biochemistry. 2nd ed. New York:

Worth, 1993.

Whitten, K.W. and K.D. Gailey. General Chemistry. 4th ed. New York: Saunders, 1992.

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