Chapter 4
Carbon and the
Molecular Diversity of
Life
Discussion Question
What
properties
make carbon
the basis of
all life?
Overview: Carbon: The Backbone
of Life
Living organisms consist mostly of carbonbased 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

Concept 4.1: Organic
chemistry is the study of
carbon compounds
Most
Urea
organic
compounds contain
hydrogen atoms in
addition to carbon
atoms
Organic Molecules and the
Origin of Life on Earth
 Stanley
Miller’s classic experiment
demonstrated the abiotic synthesis of
organic compounds
 Experiments support the idea that
abiotic synthesis of organic
compounds, perhaps near volcanoes,
could have been a stage in the origin of
life
EXPERIMENT
“Atmosphere”
CH4
Water vapor
Electrode
 Inquiry:
Can
organic
molecules form
under
conditions
believed to
simulate those
on the early
Earth?
Condenser
Cooled “rain”
containing
organic
molecules
H2O
“sea”
Sample for chemical analysis
Cold
water
4.1 Concept Check
When
Miller tried his
experiment without the
electrical discharge, no
organic compounds were
found. What might explain
this result?
Concept 4.2: Carbon atoms
can form diverse molecules
by bonding to four other
atoms



Forms 4 covalent bonds.
Molecular shape is tetrahedral.
Bonds easily to itself. When two
carbon atoms are joined by a
double bond, the atoms joined
to the carbons are in the same
plane as the carbons
Major Elements Of
Organic Molecules






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
Carbon: +4 or -4
Hydrogen: +1
Oxygen: -2
Nitrogen: -3
Molecular Diversity Arising
from Carbon Skeleton
Variation
Carbon chains form the skeletons of most
organic molecules
 Carbon chains vary in length and shape

(a) Length
Ethane
(c) Double bond position
Propane
(b) Branching
Butane
2-Methylpropane
(isobutane)
1-Butene
2-Butene
(d) Presence of rings
Cyclohexane
Animation: Carbon Skeletons
Benzene
Hydrocarbons
 Organic
molecules made of only
carbon and hydrogen.
 Hydrocarbons can undergo reactions
that release a large amount of energy
Examples
Isomers
Compounds
with the same
molecular formula but have
different structures.
Result: Different molecular
and chemical properties.
Types Of Isomers
1.
2.
3.
Structural
Geometric
Enantiomers
Structural Isomers
Different
in covalent
arrangements of their atoms.
Butane
Isobutane
Geometric Isomers
Same
covalent partnership
but differ in spatial
arrangements.
Arise from the inflexibility of
double bonds.
Enantiomers
Molecules
that are mirror
images of each other.
Usually involve an
asymmetric carbon.
Comment
Organisms
are sensitive to
even the most subtle
variations in molecular
architecture.
Example - Thalidomide
Cells
can distinguish
between two isomers.
One is an effective drug.
The other causes birth
defects.
4.2 Concept Check

In 1918, an epidemic of sleeping sickness caused
an unusual rigid paralysis in some survivors,
similar to symptoms of advanced Parkinson’s
disease. Years later, L-dopa, a chemical used to
treat Parkinson’s disease, was given to some of
these patients, as dramatized in the movie
Awakenings, starring Robin Williams. L-dopa was
remarkably effective at eliminating the paralysis,
at least temporarily. However, D-dopa was
subsequently shown to have no effect at all, as is
the case for Parkinson’s disease. In a short
essay, discuss how the effectiveness of one
enantiomer and not the other illustrates the
theme of structure and function.
Functional Groups
A
group of atoms attached to
a carbon skeleton.
Have consistent properties.
Their number and kind give
properties to the molecule.
What to focus on:
Structure
of the functional
group
Properties of the functional
group
Examples of molecules with
the functional group
Chapter 5
The Structure and
Function of Large
Biological Molecules
Focus on:
Elements
in each large
biological molecule.
How these molecules are
linked and unlinked.
Examples and functions of
each type of molecule.
Overview: The Molecules of
Life
All living things are made up of four
classes of large biological molecules:
carbohydrates, lipids, proteins, and
nucleic acids
 Macromolecules are large molecules
composed of thousands of covalently
connected atoms
 Molecular structure and function are
inseparable

Concept 5.1: 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 4.A.1The
organic molecules are polymers subcomponents
 Carbohydrates
 Proteins
 Nucleic
acids
of biological
molecules and
their sequence
determine the
properties of
that molecule.
The Synthesis and
Breakdown of Polymers
A
dehydration reaction occurs when two
monomers bond together through the loss of a
water molecule
 Polymers are disassembled to monomers by
hydrolysis, a reaction that is essentially the
reverse of the dehydration reaction
Animation: Polymers
The Diversity of Polymers
 Each
cell has thousands of
different macromolecules
 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
4.A.1The
subcomponents
of biological
molecules and
their sequence
determine the
properties of
that molecule.
4.C.1 Variation in
molecular units
provides cells with
a wider range of
functions.
5.1 Concept Check
Suppose
you are eating a
serving of fish. What
reactions must occur for the
amino acid monomers in the
protein of the fish to be
converted to new proteins in
your body?
Four Main Types of
Macromolecules or
Large Biological Molecules
Carbohydrates
Lipids
Protein
Nucleic
acids
For each Macromolecule
know the following:
Elements
it contains
Monomer units and
structures
Examples
Uses or roles
Concept 5.2: Carbohydrates
serve as fuel and building
material
Used
for fuel, building materials,
and receptors.
Made of C,H,O
General formula is CH2O
4.A.1The subcomponents
C:O ratio is 1:1
of biological molecules
and their sequence
determine the properties
of that molecule.
Types Of
Carbohydrates
Monosaccharides
Disaccharides
Oligosaccharides
Polysaccharides
Monosaccharides
Mono
- single
Saccharide - sugar
Simple sugars.
3 to 7 carbons.
Can be in linear or ring
forms.
Monosaccharides
Can
be “Aldoses” or
“Ketoses” depending on the
location of the carbonyl
group.
Examples
Glucose
Galactose
Ribose
Fructose
- OSE
Word
ending common for
many carbohydrates.
Disaccharides
Sugar
formed by joining two
monosaccharides through a
“glycosidic linkage”.
Examples
Maltose
= glucose + glucose
Lactose = glucose + galactose
Sucrose = glucose + fructose
4.C.1 Variation in
molecular units provides
cells with a wider range
of functions.
Oligosaccharides
2
- 10 joined simple sugars.
Used in cell membranes.
Polysaccharides
Many
joined simple sugars.
Used for storage or structure.
Examples:
Starch
Cellulose
Glycogen
4.C.1 Variation in
molecular units provides
cells with a wider range
of functions.
Storage Polysaccharides





Starch, a storage polysaccharide of plants, consists
entirely of glucose monomers
Plants store surplus starch as granules within
chloroplasts and other plastids
The simplest form of starch is amylose
Glycogen is a storage polysaccharide in animals
Humans and other vertebrates store glycogen mainly
in liver and muscle cells
4.C.1 Variation in
molecular units provides
cells with a wider range
of functions.
Structural Polysaccharides
 The
polysaccharide cellulose is a major
component of the tough wall of plant cells
 Like starch, cellulose is a polymer of
glucose, but the glycosidic linkages differ
 The difference is based on two ring forms
for glucose: alpha () and beta ()
4.C.1 Variation in
molecular units provides
cells with a wider range
of functions.
 glucose and  glucose
Starch
Made
of 1-4 linkages of
 glucose.
Linkage makes the molecule
form a helix.
Fuel storage in plants.
 glucose
Cellulose
Made
of 1-4 linkages of
 glucose.
Linkage makes the molecule
form a straight line.
Used for structure in plant
cell walls.
 glucose
Comment





Most organisms can digest starch (1- 4  linkage), but very few can
digest cellulose (1- 4  linkage).
Cellulose in human food passes through the digestive tract as
insoluble fiber
Some microbes use enzymes to digest cellulose
Many herbivores, from cows to termites, have symbiotic
relationships with these microbes
Another example of the link between structure and function.
4.C.1 Variation in
molecular units provides
cells with a wider range
of functions.
The structure
of the chitin
monomer


Chitin, another structural
polysaccharide, is found in
the exoskeleton of
arthropods
Chitin also provides
structural support for the
cell walls of many fungi
4.A.1The subcomponents
of biological molecules
and their sequence
determine the properties
of that molecule.
Chitin forms the exoskeleton
of arthropods.
Chitin is used to make a strong and flexible
surgical thread that decomposes after the
wound or incision heals.
5.2 Concept Check
After
a cow is given
antibiotics to treat an
infection, a vet gives the
animal a drink of “gut
culture” containing various
prokaryotes. Why is this
necessary?
5.3 Lipids are a diverse group
of hydrophobic molecules



4.A.1The subcomponents of
biological molecules and
their sequence determine
the properties of that
molecule.
Made of C,H,O
 No general formula
 C:O ratio is very high in C
Not strictly speaking a macromolecule like the others
 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
Fats and Oils
Fats
- solid at room
temperature.
Oils - liquid at room
temperature.
4.C.1 Variation in
molecular units provides
cells with a wider range
of functions.
Fats and Oils
Made
of two kinds of smaller
molecules.
Fatty
Acids
A
long carbon chain (12-18 C)
with a -COOH (acid) on one end
and a -CH3 (fat) at the other
Glycerol
Acid
Fat
Neutral Fats or
Triacylglycerols
Three
fatty acids joined to
one glycerol.
Joined by an “ester” linkage
between the -COOH of the
fatty acid and the -OH of the
alcohol.
Saturated Fats
Unsaturated Fats



Saturated - no double bonds.
 Animal fats
Unsaturated - one or more C=C bonds.
Can accept more Hydrogens.
 Plant and fish fats
Double bonds cause “kinks” in the
molecule’s shape.
4.C.1 Variation in
molecular units provides
cells with a wider range
of functions.
Animation: Fats
Question
Why
do fats usually contain
saturated fatty acids and oils
usually contain unsaturated fatty
acids?
The double bond pushes the
molecules apart, lowering the
density, which lowers the
melting point.
Fats
Differ
in which fatty
acids are used.
Used for energy
storage, cushions for
organs, insulation.
4.A.1The
subcomponents
of biological
molecules and
their sequence
determine the
properties of
that molecule.
Fats & Nutrition
A
diet rich in saturated fats may contribute
to cardiovascular disease through plaque
deposits
 Hydrogenation
is the process of converting
unsaturated fats to saturated fats by adding
hydrogen
 Hydrogenating
vegetable oils also creates
unsaturated fats with trans double bonds
 These
trans fats may contribute more than
saturated fats to cardiovascular disease
 Certain
unsaturated fatty acids are not
synthesized in the human body
 These
 These
must be supplied in the diet
essential fatty acids include the
omega-3 fatty acids, required for normal
growth, and thought to provide protection
against cardiovascular disease
Question ?
Which
has more energy, a kg
of fat or a kg of starch?
Fat - there are more C-H
bonds which provide more
energy per mass.
Phospholipids
Similar
to fats, but have only
two fatty acids.
The third -OH of glycerol is
joined to a phosphate
containing molecule.
Result
Phospholipids
have a
hydrophobic tail, but a
hydrophilic head.
When added to water
self-assembles into
micells or bilayers, an
important part of cell
membranes.
4.A.1The
subcomponents
of biological
molecules and
their sequence
determine the
properties of
that molecule.
Hydrophilic
head
Hydrophobic
tail
WATER
WATER
Steroids
Lipids
4.A.1The
subcomponents
of biological
molecules and
their sequence
determine the
properties of
that molecule.
with four fused rings.
Differ in the functional
groups attached to the rings.
Examples:
cholesterol
sex
hormones
5.3 Concept Check
 Some
amateur and professional athletes
take anabolic steroids to help them “bulk
up” or build strength. The health risks of
this practice are extensively documented.
Apart from health considerations, how do
you feel about the use of chemicals to
enhance athletic performance? Is an
athlete who takes anabolic steroids
cheating, or is such use a part of the
preparation required to succeed in
competition?
Concept 5.4: Proteins include a
diversity of structures, resulting in
a wide range of functions
 Proteins
account for more than 50% of
the dry mass of most cells
 The molecular tools of the cell.
 Made of C,H,O,N, and sometimes S.
4.A.1The
 No general formula.
subcomponents
of biological
molecules and
their sequence
determine the
properties of
that molecule.
Figure 5.15-a
Enzymatic proteins
Defensive proteins
Function: Selective acceleration of chemical reactions
Example: Digestive enzymes catalyze the hydrolysis
of bonds in food molecules.
Function: Protection against disease
Example: Antibodies inactivate and help destroy
viruses and bacteria.
Antibodies
Enzyme
Virus
Bacterium
Storage proteins
Transport proteins
Function: Storage of amino acids
Function: Transport of substances
Examples: Hemoglobin, the iron-containing protein of
vertebrate blood, transports oxygen from the lungs to
other parts of the body. Other proteins transport
molecules across cell membranes.
Examples: Casein, the protein of milk, is the major
source of amino acids for baby mammals. Plants have
storage proteins in their seeds. Ovalbumin is the
protein of egg white, used as an amino acid source
for the developing embryo.
Transport
protein
Ovalbumin
Amino acids
for embryo
4.A.1The subcomponents
of biological molecules
and their sequence
determine the properties
of that molecule.
Cell membrane
4.C.1 Variation in
molecular units provides
cells with a wider range
of functions.
Figure 5.15-b
Hormonal proteins
Receptor proteins
Function: Coordination of an organism’s activities
Example: Insulin, a hormone secreted by the
pancreas, causes other tissues to take up glucose,
thus regulating blood sugar concentration
Function: Response of cell to chemical stimuli
Example: Receptors built into the membrane of a
nerve cell detect signaling molecules released by
other nerve cells.
High
blood sugar
Insulin
secreted
Normal
blood sugar
Receptor
protein
Signaling
molecules
Contractile and motor proteins
Structural proteins
Function: Movement
Examples: Motor proteins are responsible for the
undulations of cilia and flagella. Actin and myosin
proteins are responsible for the contraction of
muscles.
Function: Support
Examples: Keratin is the protein of hair, horns,
feathers, and other skin appendages. Insects and
spiders use silk fibers to make their cocoons and webs,
respectively. Collagen and elastin proteins provide a
fibrous framework in animal connective tissues.
Actin
Muscle tissue
Myosin
100 m
4.C.1 Variation in
molecular units provides
cells with a wider range
of functions.
Connective
tissue
60 m
4.A.1The
Collagen
subcomponents
of biological
molecules and
their sequence
determine the
properties of
that molecule.
Enzymes are a type of protein that acts as a
catalyst to speed up chemical reactions
 Enzymes can perform their functions
repeatedly, functioning as workhorses that
carry out the processes of life

Animation: Enzymes
Proteins
Polypeptide
chains of Amino
Acids linked by peptide
bonds.
Amino Acid Monomers
 All
have a Carbon
with four
attachments:
 -COOH (acid)
 -NH2 (amine)
 -H
 -R (some other side
group)
Side chain (R group)
 carbon
Amino
group
Carboxyl
group
R groups
 20
different kinds:
 Nonpolar - 9 AA
 Polar - 6 AA
 Electrically Charged
Acidic - 2 AA
Basic - 3 AA
 The properties of the R groups determine
the properties of the protein.
Amino Acids
Amino Acids
Polypeptide Chains
Formed
by dehydration
synthesis between the
carboxyl group of one AA
and the amino group of the
second AA.
Produce an backbone of:
(N-C-C)X
Protein Structure and
Function



A functional protein consists of one or more
polypeptides precisely twisted, folded, and coiled
into a unique shape
The sequence of amino acids determines a
protein’s three-dimensional structure
A protein’s structure determines its function
4.B.1: Interactions between
molecules affect their structure
and function.
4.C.1 Variation in molecular
units provides cells with a
wider range of functions.
4.A.1The
subcomponents
of biological
molecules and
their sequence
determine the
properties of
that molecule.
Antibody protein
Protein from flu virus
Levels Of Protein
Structure
Organizing
the polypeptide
into its 3-D functional shape.
Primary
Secondary
Tertiary
Quaternary
Primary
Sequence
of amino
acids in the
polypeptide chain.
Many different
sequences are
possible with
20 AAs. 4.C.1 Variation in
molecular units provides
cells with a wider range
of functions.
Primary Structure
Secondary
3-D
structure formed by hydrogen
bonding between parts of the
peptide backbone.
Two main secondary
structures:

helix
pleated sheets
Tertiary
4.B.1: Interactions between
molecules affect their structure
and function.
Bonding
between the R groups.
Examples:
hydrophobic
interactions
ionic bonding
Disulfide bridges
(covalent bond)
Quaternary
When
two or more
polypeptides unite to form a
functional protein.
Example: hemoglobin,
collagen
Is Protein Structure
Important?
Denaturing Of A
Protein
Events
that cause a protein to
lose structure (and function).
biologically
inactive
Example:
pH
shifts
high salt concentrations
heat
4.A.1The
subcomponents
of biological
molecules and
their sequence
determine the
properties of
that molecule.
Protein Folding in the Cell




It is hard to predict a protein’s structure
from its primary structure
Most proteins probably go through
several stages on their way to a stable
structure
Chaperonins are protein molecules that
assist the proper folding of other
proteins
Diseases such as Alzheimer’s,
Parkinson’s, and mad cow disease are
associated with misfolded proteins
4.A.1The
subcomponents
of biological
molecules and
their sequence
determine the
properties of
that molecule.
Scientists use X-ray crystallography to
determine a protein’s structure
 Another method is nuclear magnetic
resonance (NMR) spectroscopy, which
does not require protein crystallization
 Bioinformatics uses computer programs to
predict protein structure from amino acid
sequences

EXPERIMENT
Diffracted
X-rays
X-ray
source X-ray
beam
Crystal
Digital detector
X-ray diffraction
pattern
RESULTS
RNA
DNA
RNA
polymerase II
Comment
Many
other amino acids are
possible (change the R group)
Whole new group of proteins with
new properties can be made
Genetic engineering can use
bacteria to make these new
proteins
4.C.1 Variation in
molecular units provides
cells with a wider range
of functions.
5.4 Concept Check
Comparisons
of amino acid
sequences can shed light on
the evolutionary divergence
of related species. If you were
comparing two living species,
would you expect all proteins
to show the same degree of
divergence? Why or why not?
Concept 5.5: Nucleic acids store,
transmit, and help express
hereditary information
Informational
polymers
Made of C,H,O,N and P
No general formula
3.A.1: DNA, and in
some cases RNA, is
the primary source of
heritable information.
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
3.A.1: DNA, and in
some cases RNA, is
the primary source of
heritable information.
Figure 5.25-1
DNA
1 Synthesis of
mRNA
mRNA
NUCLEUS
CYTOPLASM
Figure 5.25-2
DNA
1 Synthesis of
mRNA
mRNA
NUCLEUS
CYTOPLASM
mRNA
2 Movement of
mRNA into
cytoplasm
Figure 5.25-3
DNA
1 Synthesis of
mRNA
mRNA
NUCLEUS
CYTOPLASM
mRNA
2 Movement of
mRNA into
cytoplasm
Ribosome
3 Synthesis
of protein
Polypeptide
Amino
acids
Nucleic Acids
Polymers
of nucleotides
Nucleotides have three parts:
nitrogenous
base
pentose sugar
phosphate
Nitrogenous Bases
Rings
of C and N
The N atoms tend to take up
H+ (base).
Two types:
Pyrimidines
(single ring)
Purines (double rings)
Pentose Sugar
5-C
sugar
Ribose - RNA
Deoxyribose – DNA
RNA and DNA differ in a
–OH group on the 2nd carbon.
Nucleosides and
Nucleotides
Nucleoside
= base + sugar
Nucleotide = has the trio of
base + sugar + Pi
DNA
Deoxyribonucleic
Acid.
Makes
up genes.
Genetic information
4.A.1The
for life.
subcomponents
of biological
molecules and
their sequence
determine the
properties of
that molecule.
RNA
Ribonucleic
Acid.
Structure and protein
synthesis.
Genetic information for a few
viruses only.
Control mechanisms for
genes.
DNA and Proteins as Tape
Measures of Evolution
 The
linear sequences of nucleotides in DNA
molecules are passed from parents to
offspring
 Two closely related species are more similar in
DNA than are more distantly related species
 Molecular biology can be used to assess
evolutionary kinship
4.C.1 Variation in
molecular units provides
cells with a wider range
of functions.
DNA and RNA
More
will be said about DNA
and RNA in future lessons.
The Theme of Emergent
Properties in the Chemistry of
Life: A Review
 Higher
levels of organization result in the
emergence of new properties
 Organization is the key to the chemistry of life
Concept Check
 Construct
a table that organizes the
following terms and label the
columns and rows
PhosphoPolypeptides Monosaccdiester
harides
linkages
Triacylglycerol Peptide bonds Glycosidic
linkages
Nucleotides
Amino acids
Ester linkages
Fatty acids
Polysaccharides
Polynucleotides
Summary
Role
of hydrolysis and
dehydration synthesis
For each macromolecule, know
the following:
Elements
and monomers
Structures
Functions
Examples