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• Chapter 3
• The Chemistry of Organic Molecules
Properties of Water
• The water molecule is a polar molecule: The
opposite ends have opposite charges
• Polarity allows water molecules to form
hydrogen bonds with each other
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Four properties of water contribute to Earth’s
fitness for life
•
Four of water’s properties that facilitate an
environment for life are:
–
Cohesive behavior
–
Ability to moderate temperature
–
Expansion upon freezing
–
Versatility as a solvent
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Cohesion
• Collectively, hydrogen bonds hold water
molecules together, a phenomenon called
cohesion
• Cohesion helps the transport of water against
gravity in plants
• Adhesion is an attraction between different
substances, for example, between water and
plant cell walls
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Fig. 3-3
Adhesion
Water-conducting
cells
Direction
of water
movement
Cohesion
150 µm
Overview: Carbon: The Backbone of Life
• Although cells are 70–95% water, the rest
consists mostly of carbon-based compounds
• Carbon is unparalleled in its ability to form
large, complex, and diverse molecules
• Proteins, DNA, carbohydrates, and other
molecules that distinguish living matter are all
composed of carbon compounds
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Organic chemistry is the study of carbon
compounds
• Organic chemistry is the study of compounds
that contain carbon
• Organic compounds range from simple
molecules to colossal ones
• Most organic compounds contain hydrogen
atoms in addition to carbon atoms
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The Formation of Bonds with Carbon
• With four valence electrons, carbon can form
four covalent bonds with a variety of atoms
• This tetravalence makes large, complex
molecules possible
• In molecules with multiple carbons, each
carbon bonded to four other atoms has a
tetrahedral shape
• However, when two carbon atoms are joined
by a double bond, the molecule has a flat
shape
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Fig. 4-3
Name
(a) Methane
(b) Ethane
(c) Ethene
(ethylene)
Molecular
Formula
Structural
Formula
Ball-and-Stick
Model
Space-Filling
Model
• The electron configuration of carbon gives it
covalent compatibility with many different
elements
• The valences of carbon and its most frequent
partners (hydrogen, oxygen, and nitrogen) are
the “building code” that governs the
architecture of living molecules
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Fig. 4-4
Hydrogen
(valence = 1)
Oxygen
(valence = 2)
Nitrogen
(valence = 3)
Carbon
(valence = 4)
H
O
N
C
Isomers
• Isomers are compounds with the same molecular
formula but different structures and properties:
– Structural isomers have different covalent
arrangements of their atoms
– Geometric isomers have the same covalent
arrangements but differ in spatial
arrangements
– Enantiomers are isomers that are mirror
images of each other
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Fig. 4-7
Pentane
2-methyl butane
(a) Structural isomers
cis isomer: The two Xs are
on the same side.
trans isomer: The two Xs are
on opposite sides.
(b) Geometric isomers
L isomer
(c) Enantiomers
D isomer
The Chemical Groups Most Important in the
Processes of Life
• Functional groups are the components of
organic molecules that are most commonly
involved in chemical reactions
• The number and arrangement of functional
groups give each molecule its unique
properties
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• The seven functional groups that are most
important in the chemistry of life:
– Hydroxyl group
– Carbonyl group
– Carboxyl group
– Amino group
– Sulfhydryl group
– Phosphate group
– Methyl group
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Overview: The Molecules of Life
• All living things are made up of four classes of
large biological molecules: carbohydrates,
lipids, proteins, and nucleic acids
• Within cells, small organic molecules are joined
together to form larger molecules
• Macromolecules or Biomolecules are large
molecules composed of thousands of
covalently connected atoms
• Molecular structure and function are
inseparable
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Macromolecules are polymers, built from
monomers
• A polymer is a long molecule consisting of
many similar building blocks
• These small building-block molecules are
called monomers
• Three of the four classes of life’s organic
molecules are polymers:
– Carbohydrates
– Proteins
– Nucleic acids
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The Synthesis and Breakdown of Polymers
• A condensation reaction or more specifically
a dehydration reaction occurs when two
monomers bond together through the loss of a
water molecule
• Enzymes are macromolecules that speed up
the dehydration process
• Polymers are disassembled to monomers by
hydrolysis, a reaction that is essentially the
reverse of the dehydration reaction
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Fig. 5-2
HO
1
2
3
H
Short polymer
HO
Unlinked monomer
Dehydration removes a water
molecule, forming a new bond
HO
2
1
H
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
(b) Hydrolysis of a polymer
H
H
H2O
HO
H
Fig. 5-2a
HO
1
2
3
H
Short polymer
HO
Unlinked monomer
Dehydration removes a water
molecule, forming a new bond
HO
1
2
H
3
H2O
4
H
Longer polymer
(a) Dehydration reaction in the synthesis of a polymer
Fig. 5-2b
HO
1
2
3
4
Hydrolysis adds a water
molecule, breaking a bond
HO
1
2
3
(b) Hydrolysis of a polymer
H
H
H2O
HO
H
The Diversity of Polymers
• Each cell has thousands of different kinds of
macromolecules2 3
H
HO
• Macromolecules vary among cells of an
organism, vary more within a species, and vary
even more between species
• An immense variety of polymers can be built
from a small set of monomers
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
The Molecules of Life
• All living things are made up of four classes of
large biological molecules: carbohydrates,
lipids, proteins, and nucleic acids
• Within cells, small organic molecules are joined
together to form larger molecules
• Macromolecules are large molecules
composed of thousands of covalently
connected atoms
• Molecular structure and function are
inseparable
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Macromolecules are polymers, built from
monomers
• A polymer is a long molecule consisting of
many similar building blocks
• These small building-block molecules are
called monomers
• Three of the four classes of life’s organic
molecules are polymers:
– Carbohydrates
– Proteins
– Nucleic acids
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Carbohydrates serve as fuel and building material
• Carbohydrates include sugars and the
polymers of sugars
• The simplest carbohydrates are
monosaccharides, or single sugars
• Carbohydrate macromolecules are
polysaccharides, polymers composed of many
sugar building blocks
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Sugars
• Monosaccharides have molecular formulas
that are usually multiples of CH2O
• Glucose (C6H12O6) is the most common
monosaccharide
• Monosaccharides are classified by
– The location of the carbonyl group (as aldose
or ketose)
– The number of carbons in the carbon skeleton
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• A disaccharide is formed when a dehydration
reaction joins two monosaccharides
• This covalent bond is called a glycosidic
linkage
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Fig. 5-5
1–4
glycosidic
linkage
Glucose
Glucose
Maltose
(a) Dehydration reaction in the synthesis of maltose
1–2
glycosidic
linkage
Glucose
Fructose
(b) Dehydration reaction in the synthesis of sucrose
Sucrose
Polysaccharides
• Polysaccharides, the polymers of sugars,
have storage and structural roles
• The structure and function of a polysaccharide
are determined by its sugar monomers and the
positions of glycosidic linkages
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Fig. 5-6
Chloroplast
Mitochondria Glycogen granules
Starch
0.5 µm
1 µm
Glycogen
Amylose
Amylopectin
(a) Starch: a plant polysaccharide
(b) Glycogen: an animal polysaccharide
• Glycogen is a storage polysaccharide in
animals
• Humans and other vertebrates store glycogen
mainly in liver and muscle cells
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Fig. 5-7
(a)  and  glucose
ring structures
 Glucose
(b) Starch: 1–4 linkage of  glucose monomers
 Glucose
(b) Cellulose: 1–4 linkage of  glucose monomers
Lipids are a diverse group of hydrophobic
molecules
• Lipids are the one class of large biological
molecules that do not form polymers
• The unifying feature of lipids is having little or
no affinity for water
• Lipids are hydrophobic because they consist
mostly of hydrocarbons, which form nonpolar
covalent bonds
• The most biologically important lipids are fats,
phospholipids, and steroids
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Fats
• Fats are constructed from two types of smaller
molecules: glycerol and fatty acids
• Glycerol is a three-carbon alcohol with a
hydroxyl group attached to each carbon
• A fatty acid consists of a carboxyl group
attached to a long carbon skeleton
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Fig. 5-11
Fatty acid
(palmitic acid)
Glycerol
(a) Dehydration reaction in the synthesis of a fat
Ester linkage
(b) Fat molecule (triacylglycerol)
• Fats separate from water because
water molecules form hydrogen bonds
with each other and exclude the fats
• In a fat, three fatty acids are joined to
glycerol by an ester linkage, creating a
triacylglycerol, or triglyceride
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• Fatty acids vary in length (number of carbons)
and in the number and locations of double
bonds
• Saturated fatty acids have the maximum
number of hydrogen atoms possible and no
double bonds
• Unsaturated fatty acids have one or more
double bonds
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Fig. 5-12
Structural
formula of a
saturated fat
molecule
Stearic acid, a
saturated fatty
acid
(a) Saturated fat
Structural formula
of an unsaturated
fat molecule
Oleic acid, an
unsaturated
fatty acid
(b) Unsaturated fat
cis double
bond causes
bending
Phospholipids
• In a phospholipid, two fatty acids and a
phosphate group are attached to glycerol
• The two fatty acid tails are hydrophobic, but the
phosphate group and its attachments form a
hydrophilic head
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Hydrophobic tails
Hydrophilic head
Fig. 5-13
(a) Structural formula
Choline
Phosphate
Glycerol
Fatty acids
Hydrophilic
head
Hydrophobic
tails
(b) Space-filling model
(c) Phospholipid symbol
• When phospholipids are added to water, they
self-assemble into a bilayer, with the
hydrophobic tails pointing toward the interior
• The structure of phospholipids results in a
bilayer arrangement found in cell membranes
• Phospholipids are the major component of all
cell membranes
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Fig. 5-14
Hydrophilic
head
Hydrophobic
tail
WATER
WATER
Steroids
Proteins have many structures, resulting in a wide
range of functions
• Proteins account for more than 50% of the dry
mass of most cells
• Protein functions include structural support,
storage, transport, cellular communications,
movement, and defense against foreign
substances
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Table 5-1
Polypeptides
• Polypeptides are polymers built from the
same set of 20 amino acids
• A protein consists of one or more polypeptides
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Amino Acid Monomers
• Amino acids are organic molecules with
carboxyl and amino groups
• Amino acids differ in their properties due to
differing side chains, called R groups
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Fig. 5-UN1
 carbon
Amino
group
Carboxyl
group
Fig. 5-17
Nonpolar
Glycine
(Gly or G)
Valine
(Val or V)
Alanine
(Ala or A)
Methionine
(Met or M)
Leucine
(Leu or L)
Trypotphan
(Trp or W)
Phenylalanine
(Phe or F)
Isoleucine
(Ile or I)
Proline
(Pro or P)
Polar
Serine
(Ser or S)
Threonine
(Thr or T)
Cysteine
(Cys or C)
Tyrosine
(Tyr or Y)
Asparagine Glutamine
(Asn or N) (Gln or Q)
Electrically
charged
Acidic
Aspartic acid Glutamic acid
(Glu or E)
(Asp or D)
Basic
Lysine
(Lys or K)
Arginine
(Arg or R)
Histidine
(His or H)
Amino Acid Polymers
• Amino acids are linked by peptide bonds
• A polypeptide is a polymer of amino acids
• Polypeptides range in length from a few to
more than a thousand monomers
• Each polypeptide has a unique linear sequence
of amino acids
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Protein Structure and Function
• A functional protein consists of one or more
polypeptides twisted, folded, and coiled into a
unique shape
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• The sequence of amino acids determines a
protein’s three-dimensional structure
• A protein’s structure determines its function
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Four Levels of Protein Structure
• The primary structure of a protein is its unique
sequence of amino acids
• Secondary structure, found in most proteins,
consists of coils and folds in the polypeptide
chain
• Tertiary structure is determined by interactions
among various side chains (R groups)
• Quaternary structure results when a protein
consists of multiple polypeptide chains
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Fig. 5-21c
Secondary Structure
 pleated sheet
Examples of
amino acid
subunits
 helix
Fig. 5-21e
Tertiary Structure
Quaternary Structure
Fig. 5-21f
Hydrophobic
interactions and
van der Waals
interactions
Polypeptide
backbone
Hydrogen
bond
Disulfide bridge
Ionic bond
Fig. 5-21g
Polypeptide
chain
 Chains
Iron
Heme
 Chains
Hemoglobin
Collagen
• Quaternary structure results when two or
more polypeptide chains form one
macromolecule
• Collagen is a fibrous protein consisting of three
polypeptides coiled like a rope
• Hemoglobin is a globular protein consisting of
four polypeptides: two alpha and two beta
chains
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Nucleic acids store and transmit hereditary
information
• The amino acid sequence of a polypeptide is
programmed by a unit of inheritance called a
gene
• Genes are made of DNA, a nucleic acid
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The Roles of Nucleic Acids
• There are two types of nucleic acids:
– Deoxyribonucleic acid (DNA)
– Ribonucleic acid (RNA)
• DNA provides directions for its own replication
• DNA directs synthesis of messenger RNA
(mRNA) and, through mRNA, controls protein
synthesis
• Protein synthesis occurs in ribosomes
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Fig. 5-26-3
DNA
1 Synthesis of
mRNA in the
nucleus
mRNA
NUCLEUS
CYTOPLASM
mRNA
2
Movement of
mRNA into cytoplasm
via nuclear pore
Ribosome
3 Synthesis
of protein
Polypeptide
Amino
acids
The Structure of Nucleic Acids
• Nucleic acids are polymers called
polynucleotides
• Each polynucleotide is made of monomers
called nucleotides
• Each nucleotide consists of a nitrogenous
base, a pentose sugar, and a phosphate group
• The portion of a nucleotide without the
phosphate group is called a nucleoside
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Fig. 5-27
5 end
Nitrogenous bases
Pyrimidines
5C
3C
Nucleoside
Nitrogenous
base
Cytosine (C)
Thymine (T, in DNA) Uracil (U, in RNA)
Purines
Phosphate
group
5C
Sugar
(pentose)
Adenine (A)
Guanine (G)
(b) Nucleotide
3C
Sugars
3 end
(a) Polynucleotide, or nucleic acid
Deoxyribose (in DNA)
Ribose (in RNA)
(c) Nucleoside components: sugars
Fig. 5-27c-1
Nitrogenous bases
Pyrimidines
Cytosine (C)
Thymine (T, in DNA) Uracil (U, in RNA)
Purines
Adenine (A)
Guanine (G)
(c) Nucleoside components: nitrogenous bases
Fig. 5-27c-2
Sugars
Deoxyribose (in DNA)
Ribose (in RNA)
(c) Nucleoside components: sugars
Nucleotide Monomers
• Nucleoside = nitrogenous base + sugar
• There are two families of nitrogenous bases:
– Pyrimidines (cytosine, thymine, and uracil)
have a single six-membered ring
– Purines (adenine and guanine) have a sixmembered ring fused to a five-membered ring
• In DNA, the sugar is deoxyribose; in RNA, the
sugar is ribose
• Nucleotide = nucleoside + phosphate group
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Nucleotide Polymers
• Nucleotide polymers are linked together to build
a polynucleotide
• Adjacent nucleotides are joined by covalent
bonds that form between the –OH group on the
3 carbon of one nucleotide and the phosphate
on the 5 carbon on the next
• These links create a backbone of sugarphosphate units with nitrogenous bases as
appendages
• The sequence of bases along a DNA or mRNA
polymer is unique for each gene
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Fig. 5-28
5' end
3' end
Sugar-phosphate
backbones
Base pair (joined by
hydrogen bonding)
Old strands
Nucleotide
about to be
added to a
new strand
3' end
5' end
New
strands
5' end
3' end
5' end
3' end
Fig. 5-UN2
Fig. 5-UN2a
Fig. 5-UN2b
• Write Down the four macromolecules of life
• Their monomer, polymer and the type of
linkage that makes them up
Macro-molecules
monomer
polymer
linkage
Carbohydrates
Lipids
Ester bonds
Proteins
Nucleic Acids
Phosphodiester
bonds