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Chapter 24
The Chemistry of
Life: Organic and
Biological Chemistry
Lecture Presentation
John D. Bookstaver
St. Charles Community College
Cottleville, MO© 2012 Pearson Education, Inc.
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Organic and
BiologicalChemistry
Organic Chemistry
• Organic chemistry is the chemistry
of carbon compounds.
• Carbon has the ability to formlong chains.
• Without this property, large
biomolecules such as proteins,
lipids, carbohydrates, and nucleicacids could not form.
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Organic and
BiologicalChemistry
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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Organic and
BiologicalChemistry
Hydrocarbons
• There are four basic
types of hydrocarbons:
– Alkanes – Alkenes
– Alkynes
– Aromatic hydrocarbons
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Organic and
BiologicalChemistry
Alkanes
• Alkanes contain only single bonds.
• They are also known as saturated hydrocarbons.
– They are ―saturated‖ with hydrogens.
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Organic and
Biological
Chemistry
Formulas
• Lewis structures of alkanes look like this
(Figure 24.3).
• They are also called structural formulas.• They are often not convenient, though…,
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Organic and
Biological
Chemistry
Formulas
…so more often condensed formulas are used.
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Organic and
Biological
Chemistry
Properties of Alkanes
• The only van der Waals force is theLondon dispersion force.
• The boiling point increases with the length
of the chain.
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Organic and
Biological
Chemistry
Structure of Alkanes
• Carbons in alkanes
are sp3 hybrids.
• They have atetrahedral
geometry and
109.5 bond angles.
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Organic and
Biological
Chemistry
Structure of Alkanes
• There are only
-bonds in alkanes.
• There is freerotation about the
C—C bonds.
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Organic and
Biological
Chemistry
Isomers
Isomers havethe same
molecular
formulas, but
the atoms are
bonded in a
different order.
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Organic and
Biological
Chemistry
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 and
Biological
Chemistry
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.
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Organic and
Biological
Chemistry
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.
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Organic and
Biological
Chemistry
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 thecarbon(s) to which they
are attached.
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Organic and
Biological
Chemistry
How to Name a Compound
If there is more than
one type of
substituent in themolecule, list them
alphabetically.
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Organic and
Biological
Chemistry
Cycloalkanes
• Carbon can also form ringed structures.• Five- and six-membered rings are most stable.
– They can take on conformations in which their bondangles are very close to the tetrahedral angle.
– Smaller rings are quite strained.
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Organic and
Biological
Chemistry
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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Organic and
Biological
Chemistry
Alkenes
• Alkenes contain at least one carbon –carbondouble bond.
• They are unsaturated.
– That is, they have fewer than the maximum number
of hydrogens.
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Organic and
Biological
Chemistry
Structure of Alkenes
• Unlike alkanes, alkenes cannot rotate freely
about the double bond.
– The side-to-side overlap in the -bond makes thisimpossible without breaking the -bond.
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Organic and
Biological
Chemistry
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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Organic and
Biological
Chemistry
Nomenclature of Alkenes
• The chain is numbered so the double bond gets thesmallest 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 onopposite sides of the molecule.
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Organic and
Biological
Chemistry
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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Organic and
Biological
Chemistry
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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Organic and
Biological
Chemistry
Mechanism of Addition Reactions
In the first step, the
-bond breaks and
the new C—H bondand a cation form.
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Organic and
Biological
Chemistry
Mechanism of Addition Reactions
In the second step,
a new bond forms
between the negative
bromide ion and thepositive carbon.
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Organic and
Biological
Chemistry
Alkynes
• Alkynes contain at least one carbon –carbon
triple bond.• The carbons in the triple bond aresp-hybridized and have a linear geometry.
• They are also unsaturated.
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Organic and
Biological
Chemistry
Nomenclature of Alkynes
• The method for naming alkynes is analogous
to the naming of alkenes.• However, the suffix is -yne rather than -ene.
4-methyl-2-pentyne
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Organic and
Biological
Chemistry
Reactions of Alkynes
• Alkynes undergo many of the same reactions
alkenes do.
• As with alkenes, the impetus for reaction is thereplacement of -bonds with -bonds.
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Organic and
Biological
Chemistry
Aromatic Hydrocarbons
• Aromatic hydrocarbons are cyclic hydrocarbonsthat 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
-system.
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Organic and
Biological
Chemistry
Aromatic Nomenclature
Many aromatic hydrocarbons are known
by their common names.
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Organic and
Biological
Chemistry
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.
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Organic and
Biological
Chemistry
Reactions of Aromatic Compounds
• Due to this stabilization, aromatic compounds
do not undergo addition reactions; they
undergo substitution.
• In substitution reactions, hydrogen isreplaced by a substituent.
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Organic and
Biological
Chemistry
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.
– para-: On opposite sides of ring.
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Organic and
Biological
Chemistry
Reactions of Aromatic Compounds
Reactions of aromatic compounds often
require a catalyst.
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Organic and
Biological
Chemistry
Functional
Groups The term functional
group is used to
refer to parts of
organic moleculeswhere reactions
tend to occur.
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Organic and
Biological
Chemistry
Alcohols
• Alcohols contain one or morehydroxyl groups, —OH.
• They are named
from the parent
hydrocarbon; thesuffix is changed to
- ol and a number
designates the carbon
to which the hydroxyl
is attached.
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Organic and
Biological
Chemistry
Alcohols
• Alcohols are much more acidic than hydrocarbons. – pK a ~15 for most alcohols.
– Aromatic alcohols have pK a ~10.
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Organic and
Biological
Chemistry
Ethers
• Ethers tend to be quite unreactive.
• Therefore, they are good polar solvents.
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Organic and
Biological
Chemistry
Aldehydes
In an aldehyde, at least one hydrogen isattached to the carbonyl carbon.
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Organic and
Biological
Chemistry
Ketones
In ketones, there are two carbons bonded to
the carbonyl carbon.
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Organic and
Biological
Chemistry
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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Organic and
Biological
Chemistry
Esters
• Esters are the products of reactions between
carboxylic acids and alcohols.
• They are found in many fruits and perfumes.
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Organic and
Biological
Chemistry
Amides
Amides are formed by the reaction of
carboxylic acids with amines.
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Organic and
Biological
Chemistry
Amines
• Amines are organic bases.
• They generally have strong, unpleasant odors.
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Organic and
Biological
Chemistry
Chirality
• Carbons with four different groups attached tothem are handed, or chiral.
• These are optical isomers, or stereoisomers.
• If one stereoisomer is ―right-handed,‖ itsenantiomer is ―left-handed.‖
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Organic and
Biological
Chemistry
Chirality
• Many pharmaceuticals
are chiral.
• Often only one
enantiomer isclinically active.
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Organic and
Biological
Chemistry
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.
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Organic and
Biological
Chemistry
Amino Acids and Proteins
• Hydrogen bondingin peptide chains
causes coils and
helices in the chain.
• Kinking and foldingof the coiled chain
gives proteins a
characteristic shape.
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Organic and
Biological
Chemistry
Amino Acids and Proteins
• Most enzymesare proteins.
• The shape of the
active site
complements theshape of the
substrate on which
the enzyme acts;
hence, the ―lock-
and-key‖ model.
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Organic and
Biological
Chemistry
Carbohydrates
Simple sugars are
polyhydroxy aldehydes
or ketones.
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Organic and
Biological
Chemistry
Carbohydrates
• In solution, they form cyclic structures.
• These structures can form chains of sugars
that form structural molecules such as starch
and cellulose.
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Organic and
Biological
Chemistry
Lipids
• Lipids are a broadclass of nonpolar
organic molecules.
• The fats known astriglycerides are
lipids made from
carboxylic acids
and glycerol.
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Organic and
Biological
Chemistry
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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Organic and
Biological
Chemistry
Nucleic Acids
These combine witha phosphate to form
a nucleotide.
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