Organic and Biological Molecules Explained

Chapter 22
Organic and
Biological Molecules
AP*

AP Chemistry
 LO 2.15 The student is able to explain observations regarding the solubility of
ionic solids and molecules in water and other solvents on the basis of particle
views that include intermolecular interactions and entropic effects.
(Sec 22.5-22.6)
 LO 5.11 The student is able to identify the noncovalent interactions within and
between large molecules, and/or connect the shape and function of the large
molecule to the presence and magnitude of these interactions. (Sec 22.6)

Chapter 22
Organic Chemistry and Biochemistry
 Organic Chemistry
 The study of carbon-containing compounds and their
properties. The vast majority of organic compounds
contain chains or rings of carbon atoms.
 Biochemistry
 The study of the chemistry of living things.
Copyright © Cengage Learning. All rights reserved 3

Section 22.1
Alkanes: Saturated Hydrocarbons
Hydrocarbons
 Compounds composed of carbon and hydrogen.
 Saturated: C—C bonds are all single bonds.
alkanes [CnH2n+2]
C C
H
H
H
H
H
H

Section 22.1
Hydrocarbons
 Unsaturated: contains carbon–carbon multiple
bonds.
C C C
H H
H
H
H
H
C C C
H
H
H
H

Section 22.1
Isomerism in Alkanes
 Structural isomerism – occurs when two molecules
have the same atoms but different bonds.
 Butane and all succeeding members of the
alkanes exhibit structural isomerism.

Section 22.1
Butane

Section 22.1
Rules for Naming Alkanes
1. For alkanes beyond butane, add –ane to the Greek
root for the number of carbons.
CH3–CH2–CH2–CH2–CH2–CH3 = hexane
2. Alkyl substituents: drop the –ane and add –yl.
C2H6 is ethane
C2H5 is ethyl

Section 22.1
3. Positions of substituent groups are specified by
numbering the longest chain sequentially. The
numbering is such that substituents are at lowest
possible number along chain.
CH3
CH3–CH2–CH–CH2–CH2–CH3
1 2 3 4 5 6
3-methylhexane

Section 22.1
4. Location and name are followed by root alkane
name. Substituents in alphabetical order and use
di–, tri–, etc.
CH3 CH3
CH3–CH2–CH–CH–CH2–CH3
1 2 3 4 5 6
3,4-dimethylhexane

Section 22.1
First Ten Normal Alkanes

Section 22.1
The Most Common Alkyl
Substituents and Their
Names

Section 22.1
Name each of the following:
a)
2,2,4,5-tetramethylhexane
b)
3,6-diethyl-3-methyloctane
H3C C CH2 CH CH2 CH3
CH3
CH3 CH3
CH3
H3C C CH2 CH2 CH CH2
CH2
CH2
CH2
CH3
CH3
CH3
CH3
EXERCISE!

Section 22.1
Combustion Reactions of Alkanes
 At a high temperature, alkanes react vigorously and
exothermically with oxygen.
 Basis for use as fuels.
4 10 2 2 2
2C H ( ) + 13O ( ) 8CO ( ) + 10H O( )

g g g g

Section 22.1
Substitution Reactions of Alkanes
 Primarily where halogen atoms replace hydrogen
atoms.
4 2 3
3 2 2 2
2 2 2 3
3 2 4
CH + Cl CH Cl + HCl
CH Cl + Cl CH Cl + HCl
CH Cl + Cl CHCl + HCl
CHCl + Cl CCl + HCl




hv
hv
hv
hv

Section 22.1
Dehydrogenation Reactions of Alkanes
 Hydrogen atoms are removed and the product is an
unsaturated hydrocarbon.

Section 22.1
Cyclic Alkanes
 Carbon atoms can form rings containing only C—C
single bonds.
 General formula: CnH2n
C6H12
C4H8
C3H6

Section 22.1
The Chair and Boat Forms of Cyclohexane

Section 22.2
Alkenes and Alkynes
Hydrocarbons
 Alkenes: hydrocarbons that contain at least one
carbon–carbon double bond. [CnH2n]
CH3–CH=CH2 propene
 Alkynes: hydrocarbons containing at least one carbon–
carbon triple bond. [CnHn]
CH3–CH2–CΞC–CH3 2–pentyne

Section 22.2
Alkenes and Alkynes
Rules for Naming Alkenes
1. Root hydrocarbon name ends in –ene.
C2H4 is ethene
2. With more than 3 carbons, double bond is indicated by
the lowest–numbered carbon atom in the bond.
CH2=CH–CH2–CH3
1 2 3 4
1–butene

Section 22.2
Alkenes and Alkynes
Rules for Naming Alkynes
 Same as for alkenes except use –yne as suffix.
CH3–CH2–CΞC–CH2–CH2–CH2–CH3
3–octyne

Section 22.2
Alkenes and Alkynes
Name each of the following:
a)
2,3,5-trimethyl-2-hexene
b)
6-ethyl-3-methyl-3-octene
H3C CH CH2 C C CH3
CH3
CH3
CH3
H3C C CH CH2 CH CH2
CH2 CH2
CH3 CH3
CH3
EXERCISE!

Section 22.2
Alkenes and Alkynes
Addition Reactions
 Pi Bonds (which are weaker than the C—C bonds),
are broken, and new bonds are formed to the
atoms being added.



Section 22.2
Alkenes and Alkynes
Halogenation Reactions
 Addition of halogen atoms of alkenes and alkynes.

Section 22.3
Aromatic Hydrocarbons
 A special class of cyclic unsaturated hydrocarbons.
 Simplest of these is benzene (C6H6).
 The delocalization of the electrons makes the benzene
ring behave differently from a typical unsaturated
hydrocarbon.


Section 22.3
Benzene (Aromatic Hydrocarbon)

Section 22.3
 Unsaturated hydrocarbons generally undergo rapid
addition reactions, but benzene does not.
 Benzene undergoes substitution reactions in which
hydrogen atoms are replaced by other atoms.
Benzene

Section 22.3
More Complex Aromatic Systems

Section 22.4
Hydrocarbon Derivatives
AP Learning Objectives, Margin Notes and References
 AP Margin Notes
 Acids and bases can serve as catalysts in chemical reactions. See Appendix 7.9 “Acid Catalysis” to learn more about
this acid-catalyzed reaction mechanism.

Section 22.4
 Molecules that are fundamentally hydrocarbons but
have additional atoms or groups of atoms called
functional groups.

Section 22.4
The Common
Functional Groups

Section 22.5
Polymers
 Learning Objectives
 LO 2.15 The student is able to explain observations regarding the solubility of ionic solids and molecules in water
and other solvents on the basis of particle views that include intermolecular interactions and entropic effects.

Section 22.5
Polymers
 Large, usually chainlike molecules that are built from
small molecules called monomers.

Section 22.5
Polymers
Common
Synthetic
Polymers and
their Monomers
and Applications

Section 22.5
Polymers
Types of Polymerization
 Addition Polymerization
 Monomers “add
together” to form the
polymer, with no other
products. (Teflon®)

Section 22.5
Polymers
Types of Polymerization
 Condensation Polymerization
 A small molecule, such as water, is formed for each
extension of the polymer chain. (Nylon)

Section 22.6
Natural Polymers
 Learning Objectives
 LO 2.15 The student is able to explain observations regarding the solubility of ionic solids and molecules in water
and other solvents on the basis of particle views that include intermolecular interactions and entropic effects.
 LO 5.11 The student is able to identify the noncovalent interactions within and between large molecules, and/or
connect the shape and function of the large molecule to the presence and magnitude of these interactions.

Section 22.6
Natural Polymers
Proteins
 Natural polymers made up of -amino acids with molar
masses:
~ 6000 to > 1,000,000 g/mol
 Fibrous Proteins: provide structural integrity and
strength to muscle, hair and cartilage.

Section 22.6
Natural Polymers
Proteins
 Globular Proteins:
 Roughly spherical shape
 Transport and store oxygen and nutrients
 Act as catalysts
 Fight invasion by foreign objects
 Participate in the body’s regulatory system
 Transport electrons in metabolism

Section 22.6
Natural Polymers
α-Amino Acids
 –NH2 always attached to the α-carbon
(the carbon attached to –COOH)
C = α-carbon
R = side chains
H
C
R
COOH
H2N

Section 22.6
Natural Polymers
Bonding in α-Amino Acids
 There are 20 amino acids commonly found in proteins.

Section 22.6
Natural Polymers
Levels of Structure in Proteins
 Primary: Sequence of amino acids in the protein chain.
 Secondary: The arrangement of the protein chain in the
long molecule (hydrogen bonding determines this).
 Tertiary: The overall shape of the protein (determined
by hydrogen-bonding, dipole-dipole interactions, ionic
bonds, covalent bonds and London forces).

Section 22.6
Natural Polymers
Hydrogen Bonding in α-
Helical Arrangement of a
Protein Chain

Section 22.6
Natural Polymers
Pleated Sheet

Section 22.6
Natural Polymers
Carbohydrates
 Food source for most organisms and structural material
for plants.
 Empirical formula = CH2O
 Monosaccharides (simple sugars)
pentoses – ribose, arabinose
hexoses – fructose, glucose

Section 22.6
Natural Polymers
Some Important
Monosaccharides

Section 22.6
Natural Polymers
Carbohydrates
 Disaccharides (formed from 2 monosaccharides joined
by a glycoside linkage, a C—O—C bond between the
rings):
sucrose (glucose + fructose)
 Polysaccharides (many monosaccharide units):
starch, cellulose

Section 22.6
Natural Polymers
The Disaccharide Sucrose is Formed From α-D-glucose and
Fructose

Section 22.6
Natural Polymers
Nucleic Acids
 DNA (deoxyribonucleic acid): stores and transmits
genetic information, responsible (with RNA) for protein
synthesis.
(Molar masses = several billion)
 RNA (ribonucleic acid): helps in protein synthesis.
(Molar masses from 20,000 to 40,000 g/mol)

Section 22.6
Natural Polymers
Nucleotides
 Monomers of the nucleic acids.
 Three distinct parts:
 A five–carbon sugar, deoxyribose in DNA and ribose
in RNA.
 A nitrogen–containing organic base.
 A phosphoric acid molecule (H3PO4).

Section 22.6
Natural Polymers
Deoxyribose (in DNA)
and Ribose (in RNA)

Section 22.6
Natural Polymers
The Organic Bases Found in DNA and RNA

Section 22.6
Natural Polymers
DNA
 Key to DNA’s functioning is its double-helical structure
with complementary bases on the two strands.
 The bases form hydrogen bonds to each other.

Section 22.6
Natural Polymers
Hydrogen Bonding in DNA

Organic and Biological Molecules Explained

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