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CHAPTER 3
THE CHEMISTRY
OF ORGANIC
MOLECULES
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What are characteristics of Carbon making it such a
versatile element?
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HYDROCARBONS
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PowerPoint TextEdit Art Slides for
Biology, Seventh Edition
Neil Campbell and Jane Reece
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The synthesis and breakdown of polymers
HO
1
3
2
H
HO
Unlinked monomer
Short polymer
Dehydration removes a water
molecule, forming a new bond
HO
1
H
2
3
H2O
4
H
Longer polymer
(a) Dehydration reaction in the synthesis of a polymer
HO
1
2
3
4
Hydrolysis adds a water
molecule, breaking a bond
HO
1
2
3
H
(b) Hydrolysis of a polymer
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H
H2O
HO
H
CARBOHYDRATES








Elements
Monomers
Ratio of atoms?
Polymers
Ratio of atoms?
Functional Group
Linear vs. Ring
Purpose
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Monosaccharides are the simplest
carbohydrates
• Monosaccharides are single-unit
sugars….monomers
• These molecules typically have a formula that is a
multiple of CH2O
• What functional groups?
• What is the purpose of carbs?
• Examples include:
– Sugars, starches, cellulose
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The structure and classification of some
monosaccharides
Triose sugars
(C3H6O3)
O
H
Aldoses
C
O
Hexose sugars
(C6H12O6)
H
C
H
O
C
OH
H
C
OH
H
C
OH
H
C
OH
H
C
OH
HO
C
H
C
OH
H
H
C
OH
H
H
Ribose
H
H
C
H
C
OH
H
HO
C
H
C
OH
HO
C
H
H
C
OH
H
C
OH
H
C
OH
H
C
OH
H
Glucose
H
Galactose
H
C OH
H
C
O
H
C OH
H
C OH
C
O
O
C OH
H
C OH
HO
H
H
C OH
H
C OH
Dihydroxyacetone
H
C OH
H
C OH
H
C OH
H
H
Ribulose
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O
C
C
H
Glyceraldehyde
Ketoses
Review –
What are
compounds
with the
same number
of atoms,
same
elements, but
different
structures
called?
H
Pentose sugars
(C5H10O5)
C H
H
Fructose
GLUCOSE – GALACTOSE - FRUCTOSE
Isomers = same formula, different structure
Formula = C6H12O6
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• Many monosaccharides form rings, as shown here
for glucose
Abbreviated
structure
Figure 3.4C
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Cells link single sugars to form disaccharides
• Monosaccharides can join to form disaccharides,
such as sucrose (table sugar) and maltose (brewing
sugar)
Glucose
Glucose
Sucrose
Figure 3.5
Maltose
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Examples of disaccharide synthesis
(a)
Dehydration reaction
in the synthesis of
maltose. The bonding
of two glucose units
forms maltose. The
glycosidic link joins
the number 1 carbon
of one glucose to the
number 4 carbon of
the second glucose.
Joining the glucose
monomers in a
different way would
result in a different
disaccharide.
CH2OH
CH2OH
O
H
H
OH
H
OH
H
OH
HO
H
O
H
H
H
HO
H
OH
CH2OH
H
OH
OH
O
H
H
OH
H
CH2OH
H
1–4
1 glycosidic
linkage
HO
4
H
OH
H
H
OH
O
H
OH
O
H
H
OH
OH
H2O
Glucose
Glucose
CH2OH
O
H
(b)
Dehydration reaction HO
in the synthesis of
sucrose. Sucrose is
a disaccharide formed
from glucose and fructose.
Notice that fructose,
though a hexose like
glucose, forms a
five-sided ring.
H
OH
H
Maltose
CH2OH
CH2OH
O
H
H
OH
HO
H
HO
H
O
H
H
OH
CH2OH
OH
OH
H
H
H
1–2
glycosidic
1
linkage
Fructose
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H
2
H
HO
O
HO
H
OH
CH2OH
OH
H2O
Glucose
CH2OH
O
Sucrose
H
Polysaccharides
• Generally hundreds to thousands of monomers
• Glucose is the most common monomer of
polysaccharides
• Common polysaccharides
– Starch
– Glycogen
– Cellulose
– Chitin
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Chitin, a structural polysaccharide
H
OH
CH2OH
O OH
H
OH H
H
H
NH
C
O
CH3
(a) The structure of the
chitin monomer.
(b) Chitin forms the exoskeleton
of arthropods. This cicada
is molting, shedding its old
exoskeleton and emerging
in adult form.
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(c) Chitin is used to make a
strong and flexible surgical
thread that decomposes after
the wound or incision heals.
• Starch and glycogen are polysaccharides that
store sugar for later use
• Cellulose is a polysaccharide in plant cell walls
Starch granules in
potato tuber cells
Glycogen granules in
muscle tissue
Cellulose fibrils in
a plant cell wall
Cellulose
molecules
Figure 3.7
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Glucose
monomer
STARCH
GLYCOGEN
CELLULOSE
Starch and cellulose structures
H
O
C
CH2OH
H
4
O
H
OH
H
HO
C
H
H
C
OH
H
C
OH
H
C
OH
OH
HO
OH
H
OH
C
H
H
CH2OH
 glucose
H
O
H
OH
4
OH
1
H
HO
H
H
OH
glucose
(a)  and glucose ring structures
CH2OH
CH2OH
O
HO
O
4
1
OH
O
O
O
1
OH
4
O
1
OH
OH
OH
CH2OH
CH2OH
O
4
1
OH
O
OH
OH
(b) Starch: 1– 4 linkage of  glucose monomers
OH
CH2OH
O
HO
O
OH
1
4
OH
O
O
OH
CH2OH
(c) Cellulose: 1– 4 linkage of glucose monomers
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OH
O
O
OH
OH
CH2OH
O
OH
CH2OH
OH
Polysaccharides - CELLULOSE
• Component of plant cell walls
• 1-4 beta glucose linkage…..can form large
structure…..rigid
• Dietary fiber
Cell walls
Cellulose microfibrils
in a plant cell wall
Microfibril
About 80 cellulose
molecules associate
to form a microfibril, the
main architectural unit
of the plant cell wall.
– Soluble
0.5  m
– insoluble
Plant cells
OH CH2OH
OH
CH2OH
O O
O O
OH
OH
OH
OH
O
O O
O O
OH CH2OH
OH CH2OH
Parallel cellulose molecules are
held together by hydrogen
bonds between hydroxyl
groups attached to carbon
atoms 3 and 6.
CH2OH
OH CH2OH
OH
O
O
OH O OH
OH O OH
O
O O
O O
OH CH2OH
OH CH2OH
CH2OH
OH
OH CH2OH
O O
O O
OH
OH
OH O
O OH
O O
O
CH
OH
OH
CH
OH
2
2OH
 Glucose
monomer
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A cellulose molecule
is an unbranched 
glucose polymer.
Cellulose-digesting bacteria are found in grazing
animals such as this cow
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Blood Sugar = Glucose
Once you eat, digestion
takes place.
During this process, large
molecules are broken down
into smaller sugars.
Sugar enters your
bloodstream and this sugar is
the main source of
energy….called blood sugar,
which is simply glucose
BUT YOU DO NOT WANT
HIGH OR LOW LEVELS OF
GLUCOSE IN THE BLOOD
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Blood Sugar Chart
Fasting Value
Post Prandial
Minimum Value
Maximum Value
Value 2 hours
after consuming
glucose
Normal
Early Diabetes
70
101
100
126
Less than 140
140 to 200
Established
Diabetes
More than 126
-
More than 200
Category of a person
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High/Low Blood Sugar Levels Mean…….
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High Blood Sugar causes insulin to be released and sugar not
used will be stored as fat
Low Blood Sugar causes glucagon to be released and glycogen in
the liver will be broken down to release glucose
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Polysaccharides - GLYCOGEN
• Product of animals
• 1-4 alpha glucose linkage
• Back up supply of energy when blood sugar
drops
• In the liver
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Polysaccharides - STARCH
• Plant product
• 1-4 alpha glucoses
• Eat starch, broken down to glucose, may be
used to replenish glycogen (in liver) if it has
been used to replenish the blood sugar supply
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CHAPTER 3
THE CHEMISTRY
OF ORGANIC
MOLECULES
Lipids
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publishing
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Cummings
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LIPIDS
Fat

(triglyceride), phospholipid, steroid, wax
Characteristics of Lipids:
 Hydrophobic
Nonpolar (do not dissolve in
water)
These compounds are composed
largely of carbon and hydrogen
– They are not true polymers
– They are grouped together
because they do not mix
with water
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TRIGLYCERIDES (FATS)
• Made of glycerol and fatty acids
• Effective in storing long term energy
• May be saturated fat, monounsaturated fat, or
polyunsaturated fat
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Components of a Triglyceride (Fat)
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The synthesis and structure of a fat, or
triacylglycerol (triglyceride)
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Examples of saturated and unsaturated fats and
fatty acids
Stearic acid
(a) Saturated fat and fatty acid
Oleic acid
(b) Unsaturated fat and fatty acid
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cis double bond
causes bending
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Hydrogenation
Before
Unsaturated
Liquid
Cis
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After
Saturated
Solid
Trans
PHOSPHOLIPIDS

Glycerol with a
phosphate and 2
fatty acids =
PHOSPHOLIPID
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The structure of a phospholipid
+N(CH )
Hydrophilic head
CH2
3 3
Choline
CH2
O
O
P
–
O
Phosphate
O
CH2
CH
O
O
C
O C
CH2
Glycerol
O
Hydrophobic tails
Fatty acids
(a) Structural formula
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Hydrophilic
head
Hydrophobic
tails
(b) Space-filling model
(c) Phospholipid
symbol
Bilayer structure formed by self-assembly of
phospholipids in an aqueous environment
WATER
Hydrophilic
head
WATER
Hydrophobic
tail
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4 TYPES OF LIPIDS
Triglycerides, Phospholipids, Waxes, Steroids

Wax = carboxylic acid chain (fatty acid) joined to
alcohol chain (-OH)
 Wax = water-proof, protective covering
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STEROIDS
H3C
CH3
CH3
HO
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CH3
CH3
A comparison of functional groups of female (estradiol) and
male (testosterone) sex hormones
Estradiol
CH3
OH
HO
Female lion
CH3
OH
CH3
O
Male lion
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Testosterone
CHAPTER 3
THE CHEMISTRY
OF ORGANIC
MOLECULES
Nucleic Acids
Copyright
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2005
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Inc.
publishing
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Benjamin
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Cummings
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NUCLEIC ACIDS






Elements
Monomers
Ratio of atoms?
Polymers
Functional Group
Purpose
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Overview of Protein Synthesis
DNA ----------> RNA --------> Protein
Transcription
Translation
DNA
DNA serves as a template to make
1 Synthesis of
mRNA in the nucleus
mRNA
RNA (transcription), which then
carries the code for making a protein.
The code is deciphered to make the
protein (translation).
NUCLEUS
CYTOPLASM
2 Movement of
mRNA into cytoplasm
via nuclear pore
mRNA
Ribosome
3 Synthesis
of protein
Polypeptide
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Amino
acids
Nucleotide

This is what a nucleotide would look
like in reality…….
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The components of nucleic acids
Nitrogenous bases
Pyrimidines
5’ end
5’C
NH2
O
Nucleoside
O
Nitrogenous
base
O
O
C
O P O
Purines
CH2 O
O
3’C
O
Phosphate 3’C
Pentose
group
sugar
HC
N C C
N
N C
N
H
Adenine
A
(b) Nucleotide
OH
3’ end
(a) Polynucleotide,
or nucleic acid
O
NH2

5’C
CH
CH
5’C

O
C
C
CH3
HN
C
HN
CH
C
CH
C
C
CH
N
N
O
N
O
O
H
H
H
Cytosine Thymine (in DNA) Uracil (in RNA)
C
U
T
N
3’C
O
5’
CH
HC
N C C
NH
N C N
H
Guanine
G
Pentose sugars
HOCH2 O OH
4
H H 1’
H 3’ 2’ H
OH H
Deoxyribose (in DNA)
NH2
5’
HOCH2 O OH
4
H H 1’
H 3’ 2’ H
OH OH
Ribose (in RNA)
(c) Nucleoside components
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C
Structure of DNA
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• DNA consists of two
polynucleotides twisted
around each other in a double
helix
– The sequence of the four
kinds of nitrogenous
bases in DNA carries
genetic information
Base
pair
Nitrogenous
base (A)
Figure 3.20C
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Double Helix
Watson and Crick
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PROTEINS




What elements are in proteins?
Some common examples are:
Keratin, collagen, silk
What are the monomers of
proteins?
Proteins are involved in:
cellular structure
movement
defense
transport
communication
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An Overview of Protein Functions
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Amino Acid = Monomer of Proteins
 carbon
R
O
H
N
C
C
OH
H
H
Amino
group
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Carboxyl
group
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• Each amino acid has specific properties
Leucine (Leu)
Serine (Ser)
HYDROPHOBIC
Figure 3.12B
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Cysteine (Cys)
HYDROPHILIC
Amino acids can be linked by peptide bonds
• Cells link amino acids together by dehydration
• The bonds between amino acid monomers are called
peptide bonds
Carboxyl
group
Amino
group
PEPTIDE
BOND
Dehydration
synthesis
Amino acid
Amino acid
Figure 3.13
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Dipeptide
Polypeptides
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Making a polypeptide chain
Peptide
bond
OH
CH2
SH
CH2
H
N
H
OH
C C
CH2
H
H
N C C OH H
N C
H O
H O
H
(a)
C OH
O
DESMOSOMES
H2O
OH
DESMOSOMES
DESMOSOMES
OH
CH2
H
H
N C C
H O
N C C
H
H N C C
H O
(b)
Side chains
SH
Peptide
CH2 bond CH2
Amino end
(N-terminus)
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H O
Carboxyl end
(C-terminus)
OH
Backbone
Overview: A protein’s specific shape determines its
function
• A protein, such as lysozyme, consists of polypeptide
chains folded into a unique shape
– The shape determines the protein’s function
– A protein loses its specific function when its
polypeptides unravel
Figure 3.14A
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Figure 3.14B
A protein’s primary structure is its amino acid
sequence
Secondary structure is polypeptide coiling or
folding produced by hydrogen bonding
Primary
structure
Amino acid
Secondary
structure
Hydrogen
bond
Pleated sheet
Alpha helix
Figure 3.15, 16
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Tertiary structure is the overall shape of a
polypeptide
Quaternary structure is the relationship among
multiple polypeptides of a protein
Tertiary
structure
Polypeptide
(single subunit
of transthyretin)
Quarternary
structure
Transthyretin, with four
identical polypeptide subunits
Figure 3.17, 18
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Exploring Levels of Protein Structure:
Secondary structure
pleated sheet
O
O
H
H
Amino acid
subunits
C
C
N
C
R
C
N
C
R
H
C
C
N
C
R
H
H
H
O
H
N
C
H
C
H
O
N
C
H
R
R
R
H
C
N
C
O
H
N
O
H
C
R
H
H
O
C
N
C
R
C
H
R
N
O
H
N
H
C
R
H
R
C
O
C
C
R
C
H
H
H
C
C
H
O
H
N
O
N
O
N
H
C
C
C
H
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 helix
C
N
C
C
R
O
H
H
O
C
H
N
H
C
H
H
R
N
C
N
C
R
C
O
N
H
C
C
H
R
R
O
C
H
N
H
H
C
O
R
H
C
H
N
R
C
C
C
O
H
C
O
R
O
R
N
O
H
O
H
C
O
N
H
C
C
R
C
N
H
C
H
H
O
N
C
Exploring
of Protein
Structure:
Figure 5.20Levels
Exploring
Levels
of Protein Structure:
Tertiary
Tertiarystructure
structure
CH
CH2
Hydrogen
bond
H3C
CH3
H3C
CH3
CH
O
H
O
Hydrophobic
interactions and
van der Waals
interactions
OH C
CH2
CH2 S S CH2
Disulfide bridge
O
CH2 NH3+ -O C CH2
Ionic bond
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Polypeptide
backbone
Denaturation and renaturation of a protein
Denaturation
Normal protein
Denatured protein
Renaturation
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Overview of Protein Synthesis
DNA ----------> RNA --------> Protein
Transcription
Translation
DNA serves as a template to make
RNA (transcription), which then
carries the code for make a protein.
The code is deciphered to make the
primary structure of a protein (translation).
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Example of an enzyme-catalyzed reaction:
hydrolysis of sucrose by sucrase
CH2OH
CH2OH
O
O
H H
H
H
OH
H HO
O
+
HO
CH2OH
H
OH
Sucrase
H2O
OH H
CH2OH
O H
H
H
OH H
OH
HO
H
OH
CH2OH
O
HO
H
H HO
OH H
CH2OH
Sucrose
Glucose
Fructose
C12H22O11
C6H12O6
C6H12O6
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