Carbon and the Molecular Carbon and the Molecular Diversity of LifeDiversity of Life

Chapter 4Chapter 4

Organic chemistry is the study of carbon Organic chemistry is the study of carbon compoundscompounds

Organic chemistryOrganic chemistry -- Branch of chemistry that -- Branch of chemistry that specializes in the study of carbon compounds; includes specializes in the study of carbon compounds; includes most compounds important to life.most compounds important to life.

Great variety of structures and functions of organic Great variety of structures and functions of organic molecules are due to carbon’s ability of carbon to bond molecules are due to carbon’s ability of carbon to bond with itself and many other elements.with itself and many other elements.

Pioneers of organic chemistry began to synthesize Pioneers of organic chemistry began to synthesize organic compounds from inorganic molecules. organic compounds from inorganic molecules.

Friedrich Wohler (1828) synthesized urea.Friedrich Wohler (1828) synthesized urea. Stanley Miller (1953) demonstrated the possibility that Stanley Miller (1953) demonstrated the possibility that

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

Miller-Urey ApparatusMiller-Urey Apparatus

Carbon atoms are versatile building blocksCarbon atoms are versatile building blocks The kinds and number of bonds carbon will The kinds and number of bonds carbon will

form are determined by its form are determined by its tetravalent tetravalent electron configuration. (4 valence e-)electron configuration. (4 valence e-)

Completes its outer energy shell by Completes its outer energy shell by sharing valence electrons in four covalent sharing valence electrons in four covalent bonds. (Not likely to form ionic bonds.)bonds. (Not likely to form ionic bonds.)

Carbon atom is a central point from which Carbon atom is a central point from which the molecule branches off into four the molecule branches off into four directions; results in large, complex directions; results in large, complex molecules.molecules.

An organic molecule's 3-dimensional An organic molecule's 3-dimensional shape will affect its function.shape will affect its function.

When carbon forms four single covalent When carbon forms four single covalent bonds, the four e- orbitals angle from the bonds, the four e- orbitals angle from the carbon atom to form a tetrahedron.carbon atom to form a tetrahedron.

Methane/Ethane/EtheneMethane/Ethane/Ethene

Variation in carbon skeletons.Variation in carbon skeletons. Carbon chains may vary in:Carbon chains may vary in:

• Length.Length.• Shape (straight chain, branched, ring).Shape (straight chain, branched, ring).• Number and location of double bonds.Number and location of double bonds.• Other elements covalently bonded to available sites.Other elements covalently bonded to available sites.

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

HydrocarbonsHydrocarbons -- Molecules containing only carbon -- Molecules containing only carbon and hydrogen.and hydrogen.

Major components of fossil fuels produced from Major components of fossil fuels produced from the organic remains of organisms living millions the organic remains of organisms living millions of years ago, though they are not prevalent in of years ago, though they are not prevalent in living organisms.living organisms.

Hydrocarbon chains are hydrophobic because the Hydrocarbon chains are hydrophobic because the C-C and C-H bonds are nonpolar.C-C and C-H bonds are nonpolar.

IsomersIsomers

IsomersIsomers -- Compounds with -- Compounds with the same molecular formula the same molecular formula but with different structures but with different structures and different properties. and different properties.

1. Structural isomers1. Structural isomers -- -- Isomers that differ in the Isomers that differ in the covalent arrangement of covalent arrangement of their atoms.their atoms.

Number of possible isomers Number of possible isomers increases as the carbon increases as the carbon skeleton size increases.skeleton size increases.

May also differ in the May also differ in the location of double bonds.location of double bonds.

Isomers (cont)Isomers (cont) Geometric isomersGeometric isomers -- --

Same covalent Same covalent relationships, but relationships, but differ in spatial differ in spatial arrangements.arrangements.

Result from the fact Result from the fact that atoms cannot that atoms cannot rotate freely around rotate freely around double bonds.double bonds.

Subtle differences Subtle differences between isomers between isomers affects their biological affects their biological activity. activity.

Isomers (cont)Isomers (cont) EnantiomersEnantiomers -- Isomers that -- Isomers that

are mirror images of each are mirror images of each other.other.

When four different atoms When four different atoms or groups of atoms are or groups of atoms are bonded to the same carbon bonded to the same carbon (asymmetric carbon).(asymmetric carbon).

Two different spatial Two different spatial arrangements of the four arrangements of the four groups are mirror images.groups are mirror images.

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

L-isomer (levo/left)L-isomer (levo/left) D-isomer (dextro/right)D-isomer (dextro/right)

Thalidomide: Very different Thalidomide: Very different enantiomersenantiomers

Functional groups also contribute to the molecular diversity of life

Functional groupsFunctional groups -- Small groups of atoms -- Small groups of atoms bonded to the carbon skeleton of organic bonded to the carbon skeleton of organic molecules. Tmolecules. T

Functional groups:Functional groups: •• Have specific chemical and physical Have specific chemical and physical

properties.properties. •• Are commonly the chemically reactive Are commonly the chemically reactive

regions of the molecule.regions of the molecule. •• Behave consistently from one organic Behave consistently from one organic

molecule to another.molecule to another. • • Depending upon their number and Depending upon their number and

arrangement, determine chemical properties of arrangement, determine chemical properties of organic molecules in which they occur.organic molecules in which they occur.

Hydroxyl Group (R--OH) Functional group that Functional group that

consists of a hydrogen consists of a hydrogen atom bonded to an atom bonded to an oxygen atom, which in oxygen atom, which in turn is bonded to carbon.turn is bonded to carbon.

Is a Is a polar polar group (O-H group (O-H bond is polar covalent).bond is polar covalent).

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

Hydrogen bonds form Hydrogen bonds form between polar water between polar water molecules and hydroxyl molecules and hydroxyl group.group.

Organic compounds with Organic compounds with hydroxyl groups are hydroxyl groups are called called alcohols.alcohols.

Carbonyl Group (R--C=O)

Functional group that Functional group that consists of a carbon atom consists of a carbon atom double-bonded to oxygen (-double-bonded to oxygen (-CO).CO).

Is aIs a polar polar group (O can group (O can hydrogen bond)hydrogen bond)

Molecules with this functional Molecules with this functional group are group are water soluble.water soluble.

Is a functional group found in Is a functional group found in sugars.sugars.

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

If the carbonyl is NOT at the If the carbonyl is NOT at the end of the carbon skeleton, end of the carbon skeleton, the compound is a the compound is a ketone.ketone.

Carboxyl GroupCarboxyl Group(R—COOH)(R—COOH)

Functional group that Functional group that consists of a carbon atom consists of a carbon atom which is both double-bonded which is both double-bonded to an oxygen and single-to an oxygen and single-bonded to the oxygen of a bonded to the oxygen of a hydroxyl group.hydroxyl group.

Is a polar group and water Is a polar group and water soluble. soluble.

Since it donates protons, this Since it donates protons, this group has acidic properties. group has acidic properties.

Compounds with this Compounds with this functional group are called functional group are called carboxylic acids.carboxylic acids.

Amino GroupAmino Group (R--NH (R--NH22))

Functional group that Functional group that consists of a nitrogen atom consists of a nitrogen atom bonded to two hydrogens bonded to two hydrogens and to the carbon skeleton.and to the carbon skeleton.

Is a polar group and soluble Is a polar group and soluble in water.in water.

Acts as a weak base; the Acts as a weak base; the nitrogen can accept a nitrogen can accept a proton.proton.

Organic compounds with Organic compounds with this function group are this function group are called called amines.amines.

Sulfhydryl GroupSulfhydryl Group(R--SH)(R--SH)

Functional group Functional group which consists of an which consists of an atom of (- sulfur atom of (- sulfur bonded to an atom of bonded to an atom of hydrogen SH).hydrogen SH).

Help stabilize the Help stabilize the structure of proteins. structure of proteins.

Organic compounds Organic compounds with this functional with this functional group are called group are called thiols.thiols.

Phosphate GroupPhosphate Group(R--PO(R--PO44))

Functional group in which Functional group in which the phosphate is attached to the phosphate is attached to carbon skeleton by O.carbon skeleton by O.

Loss of two protons leaves Loss of two protons leaves the phosphate group with a the phosphate group with a negative charge; has acid negative charge; has acid properties.properties.

Polar group and soluble in Polar group and soluble in water.water.

Organic phosphates are Organic phosphates are important in cellular energy important in cellular energy storage and transfer (ATP). storage and transfer (ATP).

NomenclatureNomenclature

1 C: methane1 C: methane 2 C: ethane (C-C)2 C: ethane (C-C) 3 C: propane (C-3 C: propane (C-

C-C)C-C)

Ethene (C=C)Ethene (C=C) Ethyne (CEthyne (C==C)C)

Propanol (C-Propanol (C-C-C-OH)C-C-OH)

Propanal/Acetone Propanal/Acetone (C-C-C=O) (C-C-C=O)