Chemistry, The Central Science, 11th edition

Theodore L. Brown; H. Eugene LeMay, Jr.;

and Bruce E. Bursten

Chapter 25
Organic and
Biological Chemistry
John D. Bookstaver Organic and
Biological
St. Charles Community College Chemistry
Cottleville, MO © 2009, Prentice-Hall, Inc.
Organic Chemistry
• Organic chemistry is the chemistry
of carbon compounds.
• Carbon has the ability to form long
chains.
• Without this property, large
biomolecules such as proteins,
lipids, carbohydrates, and nucleic
acids could not form.
Organic and
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Structure of Carbon Compounds
• There are three hybridization states and
geometries found in organic compounds:
– sp3 Tetrahedral
– sp2 Trigonal planar
– sp Linear

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 Hydrocarbons

• There are four basic

types of hydrocarbons:
– Alkanes
– Alkenes
– Alkynes
– Aromatic hydrocarbons

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 Alkanes

• Alkanes contain only single bonds.

• They are also known as saturated
hydrocarbons.
– They are “saturated” with hydrogens.
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 Formulas
• Lewis structures of alkanes look like this.
• They are also called structural formulas.
• They are often not convenient, though…

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 Formulas
…so more often condensed formulas are used.

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 Properties of Alkanes

• The only van der Waals force is the London

dispersion force.
• The boiling point increases with the length Biological
Organic and

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 Structure of Alkanes

• Carbons in alkanes are sp3 hybrids.

• They have a tetrahedral geometry and
109.5° bond angles.

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Structure of Alkanes
• There are only -
bonds in alkanes.
• There is free
rotation about the
C—C bonds.

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Isomers

Isomers have
the same
molecular
formulas, but the
atoms are
bonded in a
different order.

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 Organic Nomenclature
• There are three parts to a compound name:
– Base: This tells how many carbons are in the
longest continuous chain.

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 Organic Nomenclature
• There are three parts to a compound name:
– Base: This tells how many carbons are in the
longest continuous chain.
– Suffix: This tells what type of compound it is.

Organic and
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 Organic Nomenclature
• There are three parts to a compound name:
– Base: This tells how many carbons are in the
longest continuous chain.
– Suffix: This tells what type of compound it is.
– Prefix: This tells what groups are attached to the
chain.

Organic and
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How to Name a Compound

1. Find the longest chain in

the molecule.
2. Number the chain from
the end nearest the first
substituent encountered.
3. List the substituents as a
prefix along with the
number(s) of the
carbon(s) to which they
are attached.
Organic and
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How to Name a Compound
If there is more than
one type of
substituent in the
molecule, list them
alphabetically.

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 Cycloalkanes
• Carbon can also form ringed structures.
• Five- and six-membered rings are most stable.
– They can take on conformations in which their bond
angles are very close to the tetrahedral angle.
– Smaller rings are quite strained.

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 Reactions of Alkanes
• Alkanes are rather unreactive due to
the presence of only C—C and C—H
-bonds.
• Therefore, they make great nonpolar
solvents.

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 Alkenes

• Alkenes contain at least one carbon–carbon

double bond.
• They are unsaturated.
– That is, they have fewer than the maximum number of
hydrogens.
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 Structure of Alkenes
• Unlike alkanes, alkenes cannot rotate freely
about the double bond.
– The side-to-side overlap in the -bond makes this
impossible without breaking the -bond.

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 Structure of Alkenes
This creates
geometric isomers,
which differ from
each other in the
spatial arrangement
of groups about the
double bond.

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 Properties of Alkenes

Structure also affects the physical properties

of alkenes.

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 Nomenclature of Alkenes
• The chain is numbered so the double bond gets the
smallest possible number.
• cis-Alkenes have the carbons in the chain on the
same side of the molecule.
• trans-Alkenes have the carbons in the chain on
opposite sides of the molecule.

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 Reactions of Alkenes

• One reaction of alkenes is the addition

reaction.
– In it, two atoms (e.g., bromine) add across the
double bond.
– One -bond and one -bond are replaced by two
-bonds; therefore, H is negative.
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Mechanism of Addition Reactions

• It is a two-step mechanism:
– The first step is the slow, rate-determining
step.
– The second step is fast.

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Mechanism of Addition Reactions
In the first step, the
-bond breaks and
the new C—H
bond and a cation
form.

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Mechanism of Addition Reactions
In the second step,
a new bond forms
between the
negative bromide
ion and the positive
carbon.

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 Alkynes

• Alkynes contain at least one carbon–carbon triple

bond.
• The carbons in the triple bond are sp-hybridized
and have a linear geometry.
• They are also unsaturated.
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 Nomenclature of Alkynes

4-methyl-2-pentyne

• The method for naming alkynes is analogous

to the naming of alkenes.
• However, the suffix is -yne rather than -ene.
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 Reactions of Alkynes
• Alkynes undergo many of the same reactions
alkenes do.
• As with alkenes, the impetus for reaction is
the replacement of -bonds with -bonds.

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 Aromatic Hydrocarbons

• Aromatic hydrocarbons are cyclic hydrocarbons that

have some particular features.
• There is a p-orbital on each atom.
– The molecule is planar.
• There is an odd number of electron pairs in the - Organic and
system. Biological
Chemistry
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 Aromatic Nomenclature
Many aromatic
hydrocarbons are
known by their
common names.

Organic and
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Reactions of Aromatic Compounds
• In aromatic
compounds, unlike
in alkenes and
alkynes, each pair of
-electrons does not
sit between two
atoms.
• Rather, the
electrons are
delocalized; this
stabilizes aromatic
compounds. Organic and
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Reactions of Aromatic Compounds

• Due to this stabilization, aromatic compounds

do not undergo addition reactions; they
undergo substitution.
• In substitution reactions, hydrogen is
replaced by a substituent. Organic and
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Structure of Aromatic Compounds

• Two substituents on a benzene ring could

have three possible relationships:
– ortho-: On adjacent carbons.
– meta-: With one carbon between them.
Organic and
– para-: On opposite sides of ring. Biological
Chemistry
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Reactions of Aromatic Compounds

Halogenation

Friedel-Crafts Reaction

Reactions of aromatic compounds often

require a catalyst. Organic and
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Functional Groups
The term functional
group is used to
refer to parts of
organic molecules
where reactions
tend to occur.

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 Alcohols
• Alcohols contain one or more hydroxyl groups,
—OH.
• They are named
from the parent
hydrocarbon; the
suffix is changed to
-ol and a number
designates the
carbon to which the
hydroxyl is
attached. Organic and
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Alcohols
• Alcohols are much
more acidic than
hydrocarbons.
– pKa ~15 for most
alcohols.
– Aromatic alcohols
have pKa ~10.

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 Ethers

• Ethers tend to be quite unreactive.

• Therefore, they are good polar solvents.

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Carbonyl Compounds
• The carbonyl group
is a carbon-oxygen
double bond.
• Carbonyl
compounds include
many classes of
compounds.

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 Aldehydes
In an aldehyde, at
least one hydrogen
is attached to the
carbonyl carbon.

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Ketones
In ketones, there
are two carbons
bonded to the
carbonyl carbon.

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 Carboxylic Acids
• Acids have a
hydroxyl group
bonded to the
carbonyl group.
• They are tart tasting.
• Carboxylic acids are
weak acids.

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Esters

• Esters are the

products of
reactions
between
carboxylic acids
and alcohols.
• They are found in
many fruits and
perfumes.
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 Amides
Amides are formed
by the reaction of
carboxylic acids with
amines.

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 Amines
• Amines are organic bases.
• They generally have strong, unpleasant
odors.

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 Chirality
• Carbons with four different groups attached to
them are handed, or chiral.
• These are optical isomers or stereoisomers.
• If one stereoisomer is “right-handed,” its
enantiomer is “left-handed.”

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 Chirality

S-ibuprofen

• Many pharmaceuticals are chiral.

• Often only one enantiomer is clinically
active.

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 Amino Acids and Proteins

• Proteins are polymers

of -amino acids.
• A condensation
reaction between the
amine end of one
amino acid and the
acid end of another
produces a peptide
bond. Organic and
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Chemistry
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Amino Acids and Proteins

• Hydrogen bonding in
peptide chains causes
coils and helices in the
chain.
• Kinking and folding of
the coiled chain gives
proteins a
characteristic shape.
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Amino Acids and Proteins

• Most enzymes are

proteins.
• The shape of the
active site
complements the
shape of the substrate
on which the enzyme
acts; hence, the “lock-
and-key” model. Organic and
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 Carbohydrates

Simple sugars are

polyhydroxy
aldehydes or ketones.

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Carbohydrates

• In solution, they form

cyclic structures.
• These can form chains
of sugars that form
structural molecules
such as starch and
cellulose.

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 Nucleic Acids
Two of the building blocks of
RNA and DNA are sugars
(ribose or deoxyribose) and
cyclic bases (adenine,
guanine, cytosine, and
thymine or uracil).

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Nucleic Acids
These combine with
a phosphate to form
a nucleotide.

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 Nucleic Acids

Nucleotides combine
to form the familiar
double-helix form of
the nucleic acids.

Organic and
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Chemistry
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