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Chapter 3
The Chemical Basis of Life II:
Organic Molecules
Lecture Outline
BIOLOGY
Sixth Edition
Robert J. Brooker, Eric P. Widmaier,
Linda E. Graham, Peter D. Stiling
© 2023 McGraw Hill, LLC. All rights reserved. Authorized only for instructor use in the classroom.
No reproduction or further distribution permitted without the prior written consent of McGraw Hill, LLC.
Key Concepts
• The Carbon Atom
• Synthesis and Breakdown of Organic Molecules and
Macromolecules
• Overview of the Four Major Classes of Organic Molecules
Found in Living Cells
• Carbohydrates
• Lipids
• Proteins
• Nucleic Acids
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The Carbon Atom
• Organic molecules contain carbon
• Organic molecules are abundant in living organisms
• Macromolecules are large, complex organic molecules
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Carbon
Carbon has 4 electrons in its outer
shell
Needs 4 more electrons to fill the
shell
It can make up to four bonds
• Usually single or double bonds,
but can form triple bonds
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Carbon
Carbon can form nonpolar or polar bonds
• Carbon and hydrogen have similar electronegativities, carbon-carbon and
carbon hydrogen bonds are non polar.
• Molecules with nonpolar bonds (like hydrocarbons) are not very water
soluble and are hydrophobic
• Carbon can form polar bonds
• When carbon forms polar covalent bonds with more electronegative atoms,
such as oxygen and nitrogen, the resulting molecule has regions of partial
negative and partial positive charges.
• Molecules with polar bonds are water soluble and are hydrophilic.
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Figure 3.2
Carbon can form both nonpolar and polar bonds as well as single and double bnnds.
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Functional Groups
• Organic molecules or macromolecules contain functional
groups.
• Groups of atoms with special chemical and functional
properties
• Have consistent function, regardless of the molecule they
are found in.
• Biological molecules can contain many functional groups
and a biomolecule's particular set of functional groups will
affect its properties, including structure, solubility and
reactivity.
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Table 3.1
Table 3.1 Some Biologically Important Functional Groups That Bond to carbon
Functional group* (with Formula† Examples of where Properties
shorthand notation) the group is found
Amino (–NH2) Amino (N H 2): A nitrogen atom is Amino acids Weakly basic (can accept H+);
bonded to an R group and 2
hydrogen atoms. (proteins) polar; forms part of peptide bonds
Carbonyl (–CO)‡ Ketone Carbonyl, ketone (C O): A carbon Steroids, waxes, Polar; highly chemically reactive;
atom is single-bonded to an R, R
prime and double-bonded to oxygen. proteins forms hydrogen bonds
Aldehyde (–CHO) Aldehyde (C H O): A carbon atom is Linear forms of Acidic (gives up H+ in water);
single-bonded to an R, hydrogen
atom, and double-bonded to an sugars and some forms part of peptide bonds
oxygen atom.
odor molecules
Carboxyl (–COOH) Carboxyl (C O O H): A carbon atom Amino acids, fatty Polar; forms hydrogen bonds with
is single-bonded to an R, hydroxyl
group, and double-bonded to an acids water
oxygen atom.
Hydroxyl (–OH) Steroids, alcohol, Nonpolar
Hydroxyl group (O H): An R group is
bonded to a hydroxyl group. carbohydrates, some
amino acids
*This list contains many of the functional groups that are important in biology. However, many more functional groups have been
identified by biochemists.
†R and R′ represent the remainder of the molecule.
‡A carbonyl group is C=O. In a ketone, the carbon of this group forms covalent bonds with two other carbon atoms. In an aldehyde,
the carbon is bonded to a hydrogen atom.
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Table 3.1
Table 3.1 Some Biologically Important Functional Groups That Bond to
carbon
Functional group* (with Formula† Examples of where Properties
shorthand notation) the group is found
Methyl (–CH3) May be attached to Nonpolar
Methyl (C H 3): A central carbon atom is bonded to an R group and three hydrogen atoms.
DNA, proteins, and
carbohydrates
Phosphate ( — PO24− ) Nucleic acids, ATP, Polar; weakly acidic and
Phosphate (P O 4 2 negatives): A central P group is double-bonded to an O atom and single-bonded to two O anions and an O atom that is bonded to an R group.
phospholipids negatively charged at typical pH
of living organisms
−
Sulfate ( — SO4 ) May be attached to Polar; negatively charged at
Sulfate (S O 4 negative): A central S group is double bonded to two O atoms and single bonded to an O anion and an O atom that is bonded to an R group.
carbohydrates, typical pH of living organisms
proteins, and lipids
Sulfhydryl (–COOH) Proteins that contain Polar; forms disulfide bridges in
Sulfhydryl (S H): An R group is bonded to an S atom bonded to a hydrogen atom.
the amino acid many proteins
cysteine
*This list contains many of the functional groups that are important in biology. However, many more functional groups have been
identified by biochemists.
†R and R′ represent the remainder of the molecule.
‡A carbonyl group is C=O. In a ketone, the carbon of this group forms covalent bonds with two other carbon atoms. In an aldehyde,
the carbon is bonded to a hydrogen atom.
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Isomers
• Molecules with same chemical formula but different
structures and characteristics
• Structural isomers- same atoms but different bonding
relationships
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Stereoisomers
Have identical bonding relationships but spatial positioning
between atoms differ.
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Enantiomers
Pair molecules that are mirror images of each other.
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Synthesis and Breakdown of Organic Molecules and
Macromolecules
• Some organic molecules are large macromolecules
composed of thousands or millions of atoms
• Such large molecules are formed by linking together many
smaller molecules called monomers and are known as
polymers.
• When a polymer is formed, two smaller molecules
combine through a dehydration reaction – produces a
larger organic molecule plus a water molecule.
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Polymer formation by dehydration reactions
• A molecule of water is removed each time a new
monomer is added, thus a “dehydration” reaction
• The process repeats to form long polymers
• A polymer can consist of thousands of monomers
• Dehydration is catalyzed by enzymes
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Breakdown of a polymer by hydrolysis reactions
• A molecule of water is added back each time a monomer
is released, a process called hydrolysis reaction.
• The process repeats to break down long polymer
• Hydrolysis is catalyzed by enzymes
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Four Major Classes of Organic Molecules Found in
Living Cells
• Carbohydrates
• Lipids
• Proteins
• Nucleic acids
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Carbohydrates
• Composed of carbon, hydrogen, and oxygen atoms
• Sugars are small carbohydrates that usually taste sweet.
• Sugars are used as a source of energy by living
organisms.
• The simplest sugars are monomers known
as monosaccharides.
• Pentoses
• Ribose C H O
5 10 5
• Deoxyribose (C H O ) 5 10 4
• Hexose
• Glucose (C H O )
6 12 6
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Figure 3.5a
• Depicts the bonds between atoms in
a monosaccharide in both linear and
ring forms.
• The ring is made from the linear
structure when the oxygen atom
attached to the carbon 5 forms a
covalent bond with carbon 1.
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Figure 3.5b
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Glucose
• α- and β-glucose
• Hydroxyl group of carbon 1 is above or below ring
• D- and L-glucose
• Enantiomers with mirror image structure
• D-glucose commonly found in living cells.
• L-glucose rarely found in living cells
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Glucose
• Galactose
• Hydroxyl group on carbon 4 and 1 of glucose is above the plane of
the ring instead of below it
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Disaccharides
Composed of two monosaccharides
Joined by dehydration or condensation reaction
• Glycosidic bond- the removal of a hydroxyl group from one
monosaccharide and a hydrogen atom of another, giving
rise to a water molecule and two sugars covalently bond
together through an oxygen atom.
Examples: sucrose (glucose and fructose), maltose,
lactose
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Figure 3.6
The bond formed between two sugar molecules by such a dehydration reaction is called a
glycosidic bond.
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Polysaccharides
Many monosaccharides linked together to form long
polymers called polysaccharides
The polysaccharides can be hydrolyzed to monosaccharides,
which are broken down to produce ATP.
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Polysaccharides
Starch
• Found in plant cells.
• Composed of thousands of a-D-glucose molecules linked moderately together in
branched chains.
• Store energy, are broken down to produce ATP.
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Polysaccharides
Glycogen
• Found in animal cells
• a-D- glucose molecules linked together, long, branched.
• Store energy, are broken down to produce ATP.
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Polysaccharides
Cellulose
• B-D-glucose polymer
• Linear arrangement of carbon-carbon bonds, no branching. This parallel structure in the branch
allows for the formation of hydrogen bonds between branching. Play a structural role, provide
strength to the structure of plant cell walls.
• Enzymes that break down a-d glucose in starch do not recognize cellulose. Plants can break
down starch, but not cellulose
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Figure 3.7
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Polysaccharides
Many monosaccharides linked together to form long
polymers
Examples:
• Structural –
• Chitin- a tough structural polysaccharide that forms the external
skeleton of insects and crustaceans as well as fungi
• Glycosaminoglycans- a large polysaccharides that play a
structural role in animals found in cartilage.
• Peptidoglycan- found in bacteria consists of polysaccharides that
are cross linked via peptide side chains
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Lipids
• Composed predominantly of hydrogen and carbon
atoms, and some oxygen
• Defining feature of lipids is that they are nonpolar and
therefore very insoluble in water
• Include fats, phospholipids, steroids, waxes
• Lipids comprise about 40% of the organic matter in the
average human body
• Not considered macromolecules because they are not
formed of many monomers covalently connected.
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Fats 1
• Also known as triglycerides.
• Formed by bonding:
• Glycerol (3 carbon molecule with one hydroxyl group at the end)
• 3 Fatty Acids (a chain of carbon and hydrogen atoms with a carboxyl group at
one end)
• Joined by dehydration; resulting bond is an ester bond
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Fatty acids
• Fatty acids differ regard to their lengths and the presence
of double bonds.
• Most fatty acids have an even number of carbon atoms,
with 16 and 18 being the most common.
• Fatty acids differ with regard to their presence in double
bonds.
o Saturated
o Unsaturated
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Fatty acids
Saturated – when all of the carbons in a fatty acid are linked by a single covalent
bond.
• each carbon has a maximal number of attached hydrogens.
• Carbons are saturated with respect to hydrogen
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Fatty acids
Unsaturated – contain one or more double bonds
• The C=C introduces kinks in fatty acid.
• A fatty acid with one double bond is a monounsaturated fatty acids.
• A fatty acid with two double bonds are polyunsaturated fatty acids.
• Essential fatty acids= such as Linoleic acid are necessary for good health but
cannot be synthesize by the body.
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Fatty acids
• Fats (triglycerides) contain high amounts of saturated fatty acids.
• Derives from animals
• Have a high melting point and tend to be solid at room temperature
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Figure 3.10
• Fats high in unsaturated fatty acids have low melting
points and are liquid at room temperature.
• Derived from plants.
• Example: oils
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Fats 2
• Most unsaturated fatty acids exist in nature in their cis form.
• Trans fatty acids are formed by an artificial process in which the
natural cis form is altered to a trans configuration.
• Trans fatty acids are more compact, have linear structure and
higher melting points.
• Linked to human diseases.
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Fats 2
Fats are important for energy storage
• Number of C-H bonds in fat or carbohydrate determine in
part how much energy the molecule can yield.
• 1 gram of fat stores more energy than 1 gram of glycogen
or starch because fats contain many C-H bonds whereas
carbs contain numerous C-OH bonds.
Fats can also be structural, providing cushioning that
support organs and insulation under the skin that helps
process animals during harsh weather conditions.
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Phospholipids
Formed from glycerol, two fatty acids and a phosphate
group
Phospholipids are amphipathic molecules
• Phosphate head – polar/hydrophilic
• Fatty acid tail – nonpolar/hydrophobic
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Figure 3.11
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Steroids
Four interconnected rings of carbon atoms
Usually insoluble in water
Example: Cholesterol
Tiny differences in structure can lead to profoundly different,
specific biological properties
• Estrogen is different from testosterone by having one less
methyl group, a hydroxyl group instead of a ketone group
and additional double bonds in one of its rings.
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Figure 3.12
Adam Jones/Science Source
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Waxes
• Many plants and animals produce lipids called waxes that
are secreted onto their surface
• May contain hundreds of different compounds but all
contain one or more hydrocarbons and long structures
that resemble a fatty acid attached by its carboxyl group
to another long hydrocarbon chain
• Very nonpolar and exclude water, providing a barrier to
water loss
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Proteins
Composed of carbon, hydrogen, oxygen, nitrogen, and small
amounts of other elements, notably sulfur
Building blocks of proteins are amino acids
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Table 3.3
Table 3.3 Major Categories and Functions of Proteins
Category Functions Examples
Proteins involved in Make mRNA from a DNA template; RNA polymerase catalyzes the
gene expression and synthesize polypeptides from mRNA; synthesis of RNA using DNA as a
regulation regulate genes template.
Motor proteins Initiate movement Myosin provides the contractile
force of muscles.
Defense proteins Protect organisms against disease Antibodies help destroy bacteria or
viruses.
Metabolic enzymes Increase rates of chemical reactions Hexokinase is an enzyme involved
in sugar metabolism.
Cell-signaling proteins Enable cells to communicate with Taste receptors in the tongue allow
each other and with the environment animals to taste molecules in food.
Structural proteins Support and strengthen structures Actin provides shape to the
cytoplasm of plant and animal cells.
Collagen gives strength to tendons.
Transporters Promote movement of solutes across Glucose transporters move glucose
membranes from outside cells to
inside cells, where it can be used
for energy.
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Proteins
Composed of carbon, hydrogen, oxygen, nitrogen, and small
amounts of other elements, notably sulfur
Building blocks of proteins are amino acids
• 20 different amino acids
• Common structure with variable side-chain that
determines structure and function
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Figure 3.14: Nonpolar Amino Acids only
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Figure 3.14 Polar Amino Acids – Uncharged and Charged
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Polypeptide formation
• Amino acids joined by dehydration reaction that links the
carboxyl of one amino acid to the amino group of another.
• The covalent bond between the carboxyl and amino group
is called a peptide bond.
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Polypeptide formation
• The free amino group of a polypeptide is the N-terminus
• The free carboxyl end is the C-terminus
• Proteins may be formed from one or several polypeptides
• Amino acids are numbered from the amino group to the
carboxyl group
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Proteins have a Hierarchy of Structure
Four progressive levels:
• Primary
• Secondary
• Tertiary
• Quaternary
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Figure 3.16
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Primary structure
• Amino acid sequence
• Determined by genes
• Genes carry
information for the
production of
polypeptides with
specific amino acid
sequence
• Ribonuclease
(degrades RNA) – 124
amino acids
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Secondary Structure
• Chemical and physical interactions cause protein folding
• Folding can be irregular or certain
regions can have a repeating folding
pattern called secondary structure
• Two basic types of secondary structure
are a and b sheets.
• In a helix, the polypeptide backbone
forms a repeating helical structure that
is stabilized by hydrogen bonds along
the backbone.
• In b sheets, regions of the polypeptide
backbone line parallel to each other.
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Tertiary structure
• The polypeptide folds
and refolds upon itself
to assume a complex
3d structure called the
tertiary structure.
• Includes all secondary
structure plus any
interactions involving
amino acid side
chains.
• This is the final level of
structure for a single
polypeptide chain Access the text alternative for slide images.
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Quaternary structure
Most proteins are
composed of two or more
polypeptides.
• Individual polypeptide
chains are protein
subunits.
• When proteins consist
of more than one
polypeptide, they are
said to have a
quaternary structure.
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Five factors that promote protein folding and stability
• Hydrogen bonds-> the large number of weak hydrogen
bonds within a polypeptide and between polypeptides
collectively produces a strong force that promotes protein
folding and stability.
• Ionic bonds and other polar interactions-> Some amino
acid side chains are positively or negatively charged.
Positive side changes may bind to negative side chains
via ionic bonds. Uncharged polar side chains in a protein
may bind to ionic amino acids.
• Hydrophobic effects-> some amino acid side chains are
non polar. The nonpolar amino acids are likely to be found
in the center.
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Five factors that promote protein folding and stability
• Van der Waals forces-> atoms within molecules have
temporary weak attractions for each other if they are an
optimal distance apart. These weak attractions are termed
van der Waals dispersion forces. These contribute to
tertiary and quaternary structure.
• Disulfide bridges – link the –SH groups of one amino acid
can bind to –SH group of another. This results in a
disulfide bridge, which links two amino acid chains
together. Can occur within the polypeptide or between
different polypeptides.
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Figure 3.18
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Protein-protein interactions
Many cellular processes involve steps in
which two or more different proteins
interact
Use first four factors to bind
• Hydrogen bonds
• Ionic bonds and other polar
interactions
• Hydrophobic effects
• Van der Waals forces
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Nucleic Acids
Responsible for the storage, expression, and
transmission of genetic information
Two classes
• Deoxyribonucleic acid (D N A)
• Stores genetic information encoded in
the sequence of nucleotide monomers
• Ribonucleic acid (R N A)
• Decodes D N A into instructions for
linking together a specific sequence of
amino acids to form a polypeptide
chain
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Nucleic acid monomer is a nucleotide
• Made up of phosphate group, a
five-carbon sugar (either ribose
or deoxyribose), and a single or
double ring of carbon and
nitrogen atoms known as a base
• Purines: adenine (A) &
guanine (G)
▪ Double ring of carbon
• Pyrimidines: cytosine (C) &
thymine (T)
▪ Single ring of carbon
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DNA is Composed of Two Strands of Nucleotides
• Nucleotides are covalently linked
together to form strands of DNA.
• The phosphate and sugar molecules
form the backbone of the DNA
• Bases project from the backbone
• The phosphate groups link the 3'
carbon of one nucleotide to the 5'
carbon of the next
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DNA is Composed of Two Strands of Nucleotides
• D N A molecule consists of two
strands of nucleotides coiled around
each other in a double helix
• Held together by hydrogen bonds
between a purine base in one strand
and a pyrimidine base in the opposite
strand
• A pairs with T; C pairs with G
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DNA versus RNA
DNA RNA
Deoxyribonucleic acid Ribonucleic acid
Deoxyribose Ribose
Thymine (T) Uracil (U)
Adenine (A), guanine (G), Adenine (A), guanine (G),
cytosine (C) used in both cytosine (C) used in both
2 strands, double helix Single strand
1 form Several forms
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