Biology

Sylvia S. Mader
Michael Windelspecht

Chapter 3
The Chemistry of
Organic Molecules
Lecture Outline
Dr. Aisha Al-Shatti

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 Outline
3.1 Organic Molecules

3.2 Carbohydrates

3.3 Lipids

3.4 Proteins

3.5 Nucleic Acids

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 • Organic chemistry: the chemistry of living
organisms.
• Inorganic chemistry: the chemistry of
nonliving matter.
• Many types of organic molecules can be
synthesis nowadays in the laboratory.
• The term Organic is used to identify those
molecules and compounds that contain
both carbon and hydrogen atoms.
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 3.1 Organic Molecules

• Organic molecules contain carbon and hydrogen

atoms bonded to other atoms.
Methane

• Four classes of organic molecules (biomolecules)

exist in living organisms:
▪ Carbohydrates
▪ Lipids
▪ Proteins
▪ Nucleic Acids 3-4
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 • A bacterial cell contains some
5,000 different organic molecules
where plant and animal cell has
twice that number.

• Diversity of life is possible because

diversity of the organic molecules.

• Despite their functional differences

the variety of organic molecules is
based on the unique chemical
properties of the carbon atom.

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 Inorganic versus Organic Molecules

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 The Carbon Atom
The carbon atom is small, with only 6 electrons:
two in the first shell and four in the outer shell.
Carbon can form four covalent bonds.
• Bonds with carbon, nitrogen, hydrogen,
oxygen, phosphorus and sulfur.
• The C-C bond is very stable.
• Long carbon chains, hydrocarbons, can be
formed.
• Besides single bonds, double bonds, triple
bonds, and ring structures are also possible.
• Branches may also form at any carbon atom,
making complex carbon chains.

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 The Carbon Atom
• The ability of carbon to share electrons with
other carbon atoms

• Establishes shape! In water

• Therefore function!

A long hydrocarbon
A cyclic hydrocarbon
The C−C bond is very stable and
allows the formation of long carbon Ring structure
chains
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 The Carbon Atom

• Carbon atoms can form double or triple bonds with

certain atoms (carbon, nitrogen).

• These are not as flexible as single bonds!

• Affect the structure of the molecule, and function.

• Side chains can also arise from carbon..

Ideal building block

Flexibility for biomolecules 3-9
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 The Carbon Skeleton and Functional
Groups

• The carbon chain of an organic molecule is

called its skeleton or backbone.

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 The Carbon Skeleton and Functional
Groups

• Functional groups are clusters of specific

atoms bonded to the carbon skeleton with
characteristic structures and functions.
▪ Determine the chemical reactivity and polarity
of organic molecules

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 The Carbon Skeleton and
Functional Groups
• Functional groups determine the chemical
reactivity and polarity of organic molecules.
• Example: Replacement of an H by -OH in the
2-carbon hydrocarbon ethane turns it into
ethanol, and from hydrophobic to hydrophilic.

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 The Carbon Skeleton and Functional
Groups

• Depending on its functional groups, an organic

molecule may be both acidic and hydrophilic
▪ A hydrocarbon that contains a carboxyl group
▪ Carboxyl groups ionize in solution by releasing
hydrogen ions, becoming both polar and acting
acidic!

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 • Nonpolar organic molecules are hydrophobic
(cannot dissolve in water) unless they contain a
polar functional group

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 R = remainder of molecule
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 Isomers
Isomers (Gk. Isos, “equal”) are organic molecules that have
identical molecular formulas but different arrangements of atoms.

Same molecular formula but different functional group

Different function!
Expected to have different properties and react differently in
chemical reactions.
Isomers are variations in the molecular structure of molecule.
Isomers are another example of how the chemistry of carbon leads to
variations in the structure of organic molecules. 3-16
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 The Biomolecules of Cells (1)

• Carbohydrates,
• Lipids,
• Proteins,
• Nucleic acids are
called biomolecules.

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 The Biomolecules of Cells (2)
• Usually consist of many repeating units
• Each repeating unit is called a monomer.
• A molecule composed of monomers is called a
polymer (many parts).
• Example: amino acids (monomer) are joined
together to form a protein (polymer)
• Lipids are not polymers because they contain two
different types of subunits.

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 The Biomolecules of Cells (3)

Table 3.2 Biomolecules

Category Subunits (monomers) Polymer
Carbohydrates* Monosaccharide Polysaccharide
Lipids Glycerol and fatty acids N/A
Proteins* Amino acids Polypeptide

Nucleic acids* Nucleotide DNA, RNA

*form polymers

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 Synthesis and Degradation
A dehydration reaction is a chemical reaction in
which subunits are joined together by the formation
of a covalent bond and water is produced during the
reaction.
• Used to connect monomers together to make polymers
• Example: formation of starch (polymer) from glucose
subunits (monomer)
A hydrolysis reaction is a chemical reaction in
which a water molecule is added to break a covalent
bond.
• Used to break down polymers into monomers
• Example: digestion of starch into glucose monomers
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 Synthesis and Degradation of
Biomolecules (1)

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 Synthesis and Degradation of
Biomolecules (2)

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 Synthesis and Degradation of
Biomolecules (3)

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 Synthesis and Degradation of
Biomolecules (4)

a. Synthesis of a biomolecule

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 Synthesis and Degradation of
Biomolecules (5)

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 Synthesis and Degradation of
Biomolecules (6)

[Link] of a biomolecule

[Link] of a biomolecule
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 Synthesis and Degradation of
Biomolecules (7)

b. Degradation of a biomolecule

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 Synthesis and Degradation of
Biomolecules (8)

a. Synthesis of a biomolecule

Jump to Synthesis and

Degradation of Biomolecules
(8) Long Description

b. Degradation of a biomolecule 3-28

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 Synthesis and Degradation (1)
Special molecules called enzymes are
required for cells to carry out dehydration
synthesis and hydrolysis reactions.
• An enzyme is a molecule that speeds up a
chemical reaction.
• Enzymes are not consumed in the reaction.

• Enzymes are not changed by the reaction.

• Enzymes are catalysts.

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 Synthesis and Degradation (2)
[Link] contains chitin.

a. Cell walls contain cellulose. c. Cell walls contain peptidoglycan.

(a): ©Charles Harker/Shutterstock RF; (b): ©Ingram Publishing/Alamy RF;
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 3.2 Carbohydrates
Carbohydrates (carbon – water)

Functions:

• Energy source

• Provide building material

(structural role)
Contain carbon, hydrogen, and oxygen
atoms in a 1:2:1 ratio

Varieties: monosaccharides,
disaccharides, and polysaccharides

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 Monosaccharides
A monosaccharide (GK. monos, “single”;
sacchar, “sugar”) is a single sugar molecule.
It is also called a simple sugar.
It has a backbone of 3 to 7 carbon atoms.
Examples:
• Glucose (blood sugar), fructose (fruit sugar), and
galactose
• Hexoses – six carbon atoms
• Ribose and deoxyribose (sugars contained in
nucleotides, the monomer of DNA)
• Pentoses – five carbon atoms
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 ▪ Ribose and deoxyribose (in nucleotides): they
contribute to the backbones of RNA and DNA,
respectively.
• Pentoses – five carbon atoms

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 Glucose

• Example: glucose,
galactose & fructose
(C6H12O6)
• Glucose is the major
source of cellular
energy (ATP).

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 Disaccharides
A disaccharide contains two monosaccharides joined together by
dehydration synthesis.
Examples:
• Lactose (milk sugar) is composed of galactose and glucose.
• Sucrose (table sugar) is composed of glucose and fructose.
• Maltose is composed of two glucose molecules.
• Lactose intolerant individuals lack the enzyme lactase which
breaks down lactose into galactose and glucose.

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 Synthesis and Degradation of Maltose (1)

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 Synthesis and Degradation of Maltose (2)

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 Synthesis and Degradation of Maltose (3)

monosaccharide + monosaccharide ⇄ disaccharide + water

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 Synthesis and Degradation of Maltose (4)

maltose 𝐂𝟏𝟐 𝐇𝟐𝟐 𝐎𝟏𝟏

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 Synthesis and Degradation of Maltose (5)

maltose 𝐂𝟏𝟐 𝐇𝟐𝟐 𝐎𝟏𝟏 water

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 Synthesis and Degradation of Maltose (6)

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 Synthesis and Degradation of Maltose (7)

monosaccharide + monosaccharide ⟵ disaccharide + water

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 Synthesis and Degradation of Maltose (8)

monosaccharide + monosaccharide ⇄ disaccharide + water

Jump to Synthesis and Degradation of Maltose (8) Long Description

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 Polysaccharides: Energy-Storage
and Structural Molecules (1)
A polysaccharide is a polymer of
monosaccharides.
Examples:
• Starch provides energy storage in plants.
• Glycogen provides energy storage in animals.
• Cellulose is found in the cell walls of plants.
• Most abundant organic molecule on earth
• Animals are unable to digest cellulose.
• Chitin is found in the cell walls of fungi and in the
exoskeleton of some animals.
• Peptidoglycan is found in the cell walls of bacteria.
• Monomers contain an amino acid chain.
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 Polysaccharides: Energy-Storage
and Structural Molecules (2)

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and Structural Molecules (2) Long Description
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 Polysaccharides: Energy-Storage
and Structural Molecules (3)

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 3.3 Lipids (1)
Lipids (Gk. lipos, “fat”).
Varied in structure
Large, nonpolar molecules that are insoluble in water
Functions:
• Long-term energy storage
• Structural components
• Heat retention
• Cell communication and regulation
• Protection
Varieties: fats, oils, phospholipids, steroids, waxes
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 3.3 Lipids (2)
Table 3.3 Lipids
Type Functions Human Uses
Fats Long-term energy storage Butter, lard
and insulation in animals
Oils Long-term energy storage Cooking oils
in plants and their seeds
Phospholipids Component of plasma Food additive
membrane
Steroids Component of plasma Medicines
membrane (cholesterol),
Sex hormones
Waxes Protection, prevention of Candles, polishes
water loss (cuticle of plant
surfaces), beeswax earwax

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 Triglycerides: Long-Term
Energy Storage (1)
Also called fats and oils
Functions: long-term energy storage and
insulation
Consist of one glycerol molecule linked to
three fatty acids by dehydration synthesis

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 Triglycerides: Long-Term
Energy Storage (2)
Fatty acids may be either unsaturated or saturated.

• Unsaturated – one or more double bonds between carbons

• Tend to be liquid at room temperature
• Example: plant oils
• Can have chemical groups on the same (cis) or opposite (trans) side
of the double bond
• Saturated – no double bonds between carbons
• Tend to be solid at room temperature
• Examples: butter, lard
• Trans – a triglyceride with at least one bond in a trans configuration

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 Fatty acids
• Fatty acid chains may be either:

1. Saturated:

• No double bonds between the carbon atoms + many

hydrogens as they can hold.

2. Unsaturated:

▪ Double bonds in the carbon chain + less bonded hydrogen

atoms.
• Chemical groups arranged on the same side (cis configuration) of the double bond
• Chemical groups arranged on opposite sides (trans configuration) of the double bond.

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 Triglycerides: Long-Term
Energy Storage (3)

Jump to Triglycerides: Long-Term Energy Storage (3) Long Description

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 Glycerol

• Glycerol is a 3-carbon compound with three

−OH groups.

Polar = glycerol is soluble in water

• Triglycerides have many nonpolar C−H bonds:

• Do not mix with water!!

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 Triglycerides: Long-Term
Energy Storage (4)

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 Triglycerides: Long-Term
Energy Storage (5)

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 Triglycerides: Long-Term
Energy Storage (6)

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 Triglycerides: Long-Term
Energy Storage (7)

Jump to Triglycerides: Long-Term Energy Storage (7) Long Description

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 Phospholipids: Membrane Components
The structure is similar to triglycerides.
• It consists of one glycerol molecule linked to two fatty
acids and a modified phosphate group.
• The fatty acids (tails) are nonpolar and hydrophobic.
• The modified phosphate group (head) is polar and
hydrophilic.

Function: forms plasma membranes of cells.

In water, phospholipids aggregate to form a lipid
bilayer (double layer).
• Polar phosphate heads are oriented towards the water.
• Nonpolar fatty acid tails are oriented away from water.
• Nonpolar fatty acid tails form a hydrophobic core.
• Kinks in the tails keep the plasma membrane fluid across a
range of temperatures.
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 Phospholipids Form Membranes

Jump to Phospholipids Form

Membranes Long Description

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 The presence of kinks in the
tails causes the plasma
membrane to be fluid across
a range of temperatures
found in nature.

A plasma membrane is
essential to the structure and
function of a cell

This signifies the

importance of phospholipids
to living organisms.

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 Steroids: Four Fused Carbon Rings
They are composed of four fused carbon rings.
• Various functional groups attached to the carbon skeleton
Functions: component of animal cell membrane,
regulation
Examples: cholesterol, testosterone, estrogen
• Testosterone and estrogen are sex hormones differing
only in the functional groups attached to the same carbon
skeleton.

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 Steroid Diversity

© Ernest A. Janes/Bruce Coleman/Photoshot

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 Cholesterol
Cholesterol is the precursor molecule for several other steroids.
Cholesterol can also contribute to circulatory disorders.

• Functions:

 Essential component of an animal cell’s plasma

membrane

• Provides physical stability

 Regulation

• Examples: cholesterol, testosterone, estrogen

• Cholesterol is a component of an animal cell’s plasma membrane,

and is the precursor of the steroid hormone.
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 Waxes (1)
Long-chain fatty acids connected to carbon
chains containing alcohol functional groups
Solid at room temperature
Waterproof
Resistant to degradation
Function: protection
Examples: earwax (contains cerumen), plant
cuticle, beeswax
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 Waxes (2)

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 3.4 Proteins
(Gk. proteios, “first place”)

Primary importance to
the structure and function of cells

50% of the dry weight

of most cells consists of proteins

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 3.4 Proteins

A protein is a polypeptide that has folded into a

particular shape, which is essential for its proper
functioning.

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 Proteins are polymers of amino acids linked
together by peptide bonds.
• A peptide bond is a covalent bond between amino acids.
• As much as 50% of the dry weight of most cells consists
of proteins.
• Several hundred thousand have been identified.
Two or more amino acids joined together are called
peptides.
• Long chains of amino acids joined together are called
polypeptides.

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 Functions of Proteins
Metabolism
• Most enzymes are proteins that act as catalysts to accelerate chemical
reactions within cells.
Support
• Some proteins have a structural function, for example, keratin and
collagen.
Transport
• Membrane channel and carrier proteins regulate what substances enter and
exit cells. Hemoglobin protein transports oxygen to tissues and cells.
Defense
• Antibodies are proteins of our immune system that bind to antigens and
prevent them from destroying cells.
Regulation
• Hormones are regulatory proteins that influence the metabolism of cells.
Motion
• Microtubules move cell components to different locations. Actin and myosin
contractile proteins allow muscles to contract. 3-70
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 Amino Acids: Protein Monomers (1)
There are 20 different common amino acids.
Amino acids differ by their R, or variable groups,
which range in complexity.

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 Amino Acids: Protein Monomers (2)

often covalently
connects one chain
of
amino acids to
another by a
disulfide bond

Jump to Amino Acids:

Protein Monomers (2)
Long Description
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⚫ A peptide bond is a covalent
bond between 2 a.a
⚫ COOH of one a.a covalently
bonds to the NH2 of the next
a.a

⚫ Two AAs– Dipeptide

⚫ Three AAs– Tripeptide
⚫ Many AAs– Polypeptide

amino group acidic group peptide bond

dehydration reaction

hydrolysis reaction

amino acid amino acid water

dipeptide

40
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 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

Oxygen is more electronegative than

nitrogen

The polarity of the peptide bond:

• Hydrogen bonding is possible between the −CO of

one amino acid and the −NH of another amino acid
in a polypeptide.
• Hydrogen bonding influences the structure, or shape,
of a protein.

⚫ Characteristics of a protein determined by composition and

sequence of AA’s
⚫ A protein may contain more than one polypeptide chain
⚫ Virtually unlimited number of proteins 3-74
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 Shapes of Proteins and Levels of
Protein Structure
Proteins cannot function properly unless they fold
into their proper shape.
• When a protein loses it proper shape, it said to be
denatured.
• Exposure of proteins to certain chemicals, a change in pH, or high
temperature can disrupt protein structure.

Proteins can have up to four levels of structure:

• Primary
• Secondary
• Tertiary
• Quaternary
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 Four Levels of Protein Structure (1)
Primary level
• Primary level is the linear sequence of amino acids.
• Hundreds of thousands of different polypeptides can be
built from just 20 amino acids.
• Changing the sequence of amino acids can produce
different proteins.
Secondary level
• Secondary level is characterized by the presence of alpha
helices and beta (pleated) sheets held in place with
hydrogen bonds.
Tertiary level
• Tertiary level is the overall three-dimensional shape of a
polypeptide.
• It is stabilized by the presence of hydrophobic interactions,
hydrogen, ionic, and covalent bonding.
Quaternary level
• Quaternary level consists of more than one polypeptide. 3-76
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 Levels of Protein Structure
• Proteins cannot function properly unless they
fold into their proper shape.

Shape loss

• Proteins can have up to four levels of structure: • Certain chemicals

▪ Primary • Change in pH
▪ Secondary • High temperature
44
▪ Tertiary
3-78
▪ Quaternary
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 Four Levels of Protein Structure

▪ Primary
• The sequence of amino acids

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 ▪ Secondary
• The way the amino acid chain coils or folds.

Two basic
patterns of a.a
structure

• Characterized by the presence of alpha () helices and beta ()

(pleated) sheets held in place with hydrogen bonds.
• Fibrous proteins (keratin) are structural proteins with helices
and/or pleated sheets that hydrogen bond to one another. 3-81
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 Examples of Fibrous Proteins

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 Tertiary
• Final overall three-dimensional shape of a polypeptide

• Stabilized by the presence of:

1. hydrophobic interactions

2. Strong disulfide linkages help maintain the tertiary shape.

3. Hydrogen bonding

4. Ionic bonding

5. covalent bonding.

• Globular proteins tend to ball up into rounded shapes

46
• E.g. enzymes 3-83
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 • Quaternary
• Consists of more than one polypeptide.

• Hemoglobin is globular protein with a

quaternary structure of four polypeptides;
each polypeptide has a primary, secondary,
and tertiary structure

Multiple subunits!!!

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 Four Levels of Protein Structure (2)

Primary structure
This level of structure is
determined by the linear
sequence of amino acids,
coded for in the genes of
the DNA.

Secondary Structure
Hydrogen bonding
between amino acids
causes the polypeptide
to form an alpha helix
or a pleated sheet.

Tertiary Structure
Interactions of amino acid side
chains with water, covalent
bonding between R groups,
and other chemical
interactions determine the
folded three-dimensional
shape of a protein.

Quaternary Structure

This level of structure occurs

when two or more folded
polypeptides interact to
perform a biological function.

Jump to Four Levels of Protein Structure (2) Long Description 3-87

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 The Importance of Protein Folding
and Protein-Folding Diseases
Chaperone proteins help proteins fold into their
normal shapes and may also correct misfolding of
new proteins.
• Defects in chaperone proteins may play a role in
several human diseases, such as Alzheimer’s
disease and cystic fibrosis.
Prions are misfolded proteins that have been
implicated in a group of fatal brain diseases known
as TSEs.
• Mad cow disease is one example of a TSE.
• Prions are believed to cause other proteins to fold the
wrong way.
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 3.5 Nucleic Acids
• Each cell has a storehouse of information
that specifies how a cell should behave,
respond to the environment and divided to
make a new cell.

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 3.5 Nucleic Acids
Nucleic acids are polymers of nucleotides.
Two varieties of nucleic acids:
• DNA (deoxyribonucleic acid)
• Genetic material that stores information for its own
replication and for the sequence of amino acids in
proteins

• RNA (ribonucleic acid)

• Performs a wide range of functions within cells which
include protein synthesis and regulation of gene
expression
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 Structure of a Nucleotide
Each nucleotide is composed of three parts:
• A phosphate group
• A pentose sugar
• A nitrogen-containing (nitrogenous) base

[Link] structure

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 Nucleotides (1)
There are five types of nucleotides found in
nucleic acids.
• DNA contains adenine, guanine, cytosine,
and thymine.
• RNA contains adenine, guanine, cytosine,
and uracil.

Nucleotides are joined together by

a series of dehydration synthesis
reactions to form a linear molecule
called a strand, which is a
sequence of nucleotides.

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 Nucleotides (2)

a. Nucleotide structure b. Deoxyribose versus ribose

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 Nucleotides (3)

c. Pyrimidines versus purines

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 Nucleotides (4)

a. Nucleotide structure b. Deoxyribose versus ribose

c. Pyrimidines versus purines

Jump to Nucleotides (4) Long Description

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 Structure of DNA and RNA (1)
The backbone of the nucleic acid strand is
composed of alternating sugar-phosphate
molecules.
RNA is predominately a single-stranded molecule,
whereas DNA is a double-stranded molecule.
• DNA is composed of two strands held together by
hydrogen bonds between the nitrogen-containing bases.
The two strands twist around each other, forming a
double helix.
• The nucleotides may be in any order within a strand but
between strands:
• Adenine (purine) makes hydrogen bonds with thymine
(pyrimidine).

• Cytosine (pyrimidine) makes hydrogen bonds with guanine

(purine).

• The bonding between the nitrogen-containing bases in

DNA is referred to as complementary base pairing.
• The number of A + G (purines) always equals the number of
T + C (pyrimidines).
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 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

Fig. 3.19
RNA Structure
N O
N
G N
P
N
NH2
S
H Nitrogen-containing
N bases
O O
P U
N
CH3
S

Backbone
N NH2
P
N A N
S N
C Cytosine S Ribose
G Guanine A Adenine
O N NH2
P Phosphate U Uracil
P C
N
S

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 DNA Structure

Complementary
Base Pairing in
DNA
Jump to DNA Structure
(a): ©Molekuul/SPL/age footstock RF Long Description
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 Structure of DNA and RNA (2)

Table 3.4 DNA Structure Compared to RNA Structure

DNA RNA
Sugar Deoxyribose Ribose
Adenine, guanine, Adenine, guanine, uracil,
Bases
thymine, cytosine cytosine
Strands Double stranded with
Single stranded
base pairing

Helix Yes No

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 ATP (Adenosine Triphosphate)
ATP (adenosine triphosphate) is a nucleotide composed of
adenine and ribose (adenosine) and three phosphates.
ATP is a high-energy molecule due to the presence of the last
two unstable phosphate bonds, which are easily broken.
Hydrolysis of the terminal phosphate bond yields:
• The molecule ADP (adenosine diphosphate)
• An inorganic phosphate, P
• Energy to do cellular work
• The hydrolysis of the ATP molecule can be coupled with chemically
unfavorable reactions in the cell to allow the reactions to proceed.
• Example: key steps in the synthesis of carbohydrates and proteins, and
muscle contraction and nerve impulse conduction

ATP is therefore called the energy currency of the cell.

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 A Special Nucleotide: ATP

• ATP (adenosine triphosphate) is

composed of adenine, ribose, and
three phosphates.

• ATP is a high-energy molecule due to

the presence of the last two unstable
phosphate bonds.
• Hydrolysis of the terminal phosphate
bond yields:
▪ The molecule ADP (adenosine
diphosphate)
▪ An inorganic phosphate
▪ Energy to do cellular work
• ATP is called the energy currency of the
cell. 3-102
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 ATP

Jump to ATP Long Description

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