LECTURE PRESENTATIONS

For BIOLOGY, TWELFTH EDITION

Sylvia S. Mader, Michael Windelspecht
Michael Windelspecht

Chapter 3

The Chemistry of
Organic Molecules

Lectures by Dr. Sabika Allehdan, PhD

Erin Barley

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 Chapter Outline

3.1 Organic Molecules

3.2 Carbohydrates
3.3 Lipids
3.4 Proteins
3.5 Nucleic Acids

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 3.1 Organic Molecules
• Organic molecules contain both carbon and
hydrogen atoms.
• Four classes of organic molecules (biomolecules)
exist in living organisms:
• Carbohydrates
• Lipids
• Proteins
• Nucleic Acids
• Functions of the four biomolecules in the cell are
diverse.

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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.
• Like octane molecules.
• Besides single bonds, double bonds, triple bonds and ring
structures are also possible.

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 The Carbon Skeleton and Functional
Groups
• The carbon chain of an organic molecule is
called its skeleton or backbone.
• 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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 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
• Carboxyl group (-COOH) is highly polar.
• In water it ionizes and releases H+ ions in
solution, so acting as acid.
• -COOH -COO- + H+
• Attached group not only determine polarity of
an organic molecule but also the type of
reaction.

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 Functional Groups
There are six functional
groups

• Hydroxyl group
• Carbonyl group
• Carboxyl group
• Amino group
• Sulfhydryl group
• Phosphate group

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 Hydroxyl Group
• Composed of a hydrogen atom bonded to an
oxygen atom: -OH
• Organic molecules containing a hydroxyl group
are known as alcohols.

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 Carbonyl Group
• Composed of a carbon atom double-bonded to an
oxygen atom: C=O

• If carbonyl group at the end of the skeleton: aldehyde.

• If carbonyl group in middle of the skeleton: ketone.

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 Carboxyl Group
• Composed of an C atom double bonded to O and
single bonded to a hydroxyl group
• Organic molecules containing a carboxyl group are known
as carboxylic acids

• Alcohol when react with carboxyl group form fatty acids

• Carboxyl when react with amino group form amino acids

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 Amino Group
• Composed of a N atom covalently bonded to two
H atoms: -NH2
• Organic molecules containing an amino group
are known as amines

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 Sulfhydryl Group
• Composed of a S atom covalently bonded to a H
atom: -SH
• Organic molecules containing a sulfhydryl group
are known as thiols.
• Forms disulfide bonds.
• SH groups stabilize the structure of proteins.

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 Phosphate Group
• An ion composed of a phosphate ion covalently attached by
one of its O atoms to the carbon skeleton
• Can release one or two hydrogen ions, producing ionized
forms with 1 or 2 units of negative charge
• Transfers energy between organic molecules (e.g., ATP)

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 Isomers
• Isomers are organic molecules that have identical
molecular formulas but different arrangements of
atoms. e.g., glucose and fructose and galactose; all are
C6H12O6. e.g., glyceraldehyde and dihydroxyacetone;
both are C3H6O3.

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 The Biomolecules of Cells
• Carbohydrates, lipids, proteins, and nucleic acids
are called biomolecules.
• 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 (glycerol and fatty acids).

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 The Biomolecules of Cells

Biomolecules Subunits (monomers) Polymer

Carbohydrates* Monosaccharide Polysaccharide
Lipids Glycerol and fatty acids Fat
Proteins* Amino acids Polypeptide
Nucleic acids* Nucleotide DNA, RNA
* Form polymers

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 Synthesis of a Biomolecule
• Synthesis of a biomolecule is achieved by the
condensation of monomers through a reaction
called condensation reaction or dehydration
synthesis.
• During dehydration synthesis, a water is removed,
and a bond is made (synthesis).
• a. When two monomers join, a hydroxyl (— OH) group is
removed from one monomer and a hydrogen (— H) is
removed from the other.
• b. This produces water.

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 Synthesis of a Biomolecule

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 Degradation of Biomolecules
• Degradation of a biomolecule is achieved by
opposite type of reaction called hydrolysis.

• Hydrolysis reactions break down polymers in

reverse of dehydration; a hydroxyl (— OH) group
from water attaches to one monomer and
hydrogen (— H) attaches to the other.

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 Degradation of Biomolecules

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 Synthesis and Degradation of
Biomolecules

• 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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 3.2 Carbohydrates
• Functions of carbohydrates:
• Immediate energy source in cells.
• Play a role in cell structure (Provide building
material)

• Majority of carbohydrates have a C:H:O ratio of

1:2:1.

• Range from a single sugar (monomer),

disaccharides, and polysaccharides (polymer).

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 Monosaccharides
• Single sugar molecules (simple sugars) – cannot be
broken down by hydrolysis
• Have a backbone of 3 to 7 carbon atoms
• Play a central role in energy storage
• Examples
• Hexoses - Six carbons
• Glucose (blood sugar), fructose (fruit sugar),
and galactose
• Pentoses – Five carbon atoms
• Ribose (sugar found in RNA) and deoxyribose
• (sugar found in DNA)

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 Monosaccharides

Large number of -OH group, this polar group gives solubility in water

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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

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 Polysaccharides: Energy-Storage
• A polysaccharide is a polymer of monosaccharides.
• Energy storage molecules.
• When energy is required, polysaccharide is broken
into sugar molecules
• Examples of polysaccharide
• Starch provides energy storage in plants.
• There are two forms of starch:
• Amylose, which is unbranched
• Amylopectin, which is branched
• Plant cells store starch as granules in amyloplasts
• The helical shape of the polysaccharides exposes the sugar
linkages to the hydrolytic enzymes that can break them down
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 Structure of Starch

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 Polysaccharides: Energy-Storage

• Glycogen provides energy storage in animals and

human
• Similar in structure to plant starch but highly
branched polymer of glucose molecules.
• Stored mainly in liver and muscle cells
• Polysaccharides serve as storage molecules
because,
they are not as soluble in water
• They are much larger than a simple sugar

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 Structure of Glycogen

Insulin converts glucose to glycogen, whereas glucagon

converts glycogen to glucose.

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 Polysaccharides: Structural Molecules

• Cellulose is the structural component of plant cell

walls (fibers)
• Most abundant organic molecule on earth
• Animals are unable to digest cellulose
• In ruminants (cow, cattle, goats), microorganisms
can break down cellulose.
• In humans, cellulose serves as dietary fiber, which
maintains regularity of fecal elimination.

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 Structure of Cellulose

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 Polysaccharides: Structural Molecules
• Chitin is a polymer of glucose
• Each glucose with an amino group.
• Very resistant to wear and digestion.
• Found in fungal cell walls and in the exoskeletons of crabs
and related animals (e.g., lobsters, scorpions, and insects)
• Human uses
• Coating seeds with chitin - protects them from attack by
soil fungi.
• In medicine as strong and flexible thread.
• Production of various foods (emulsifying and food
additive).

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 Structural of Chitin

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 Polysaccharides: Structural Molecules

• Peptidoglycan is more complex; long chain of

glucose monomers and each monomer has an
amino acid chain.

• It found in the cell walls of bacteria.

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 Polysaccharides: Structural Molecules

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 3.3 Lipids
• Large, nonpolar molecules that are insoluble
in water.
• Varied in structure - consist mainly of C and H.
• Functions:
• Long-term energy storage
• Structural components
• Heat retention
• Cell communication and regulation
• Protection
• Varieties: fats, oils, phospholipids, steroids, waxes.
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 Lipids
Type Functions Human Uses
Fats Long-term energy storage and Butter, lard
insulation in animals

Oils Long-term energy storage Cooking oils

in plants and their seeds

Phospholipids Component of plasma membrane Food additive

Steroids Component of plasma membrane Medicines

(cholesterol), Sex hormones

Waxes Protection, prevention of water Candles, polishes

loss (cuticle of plant surfaces),
beeswax, and earwax

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 Triglycerides: Long-Term Energy Storage
• Also called fats and oils
• Functions: long-term energy storage and
insulation
• Structure = glycerol + three fatty acids
• Glycerol: a 3-carbon compound with three -OH groups
• Fatty acid: molecule that contains a hydrocarbon chain
and ends with an acid group
• The 3 fatty acids of a triglyceride are not necessarily the
same

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 Triglycerides: Long-Term Energy Storage
• Fatty acids may be either unsaturated or
saturated
• Saturated fats
•No double bonds between carbons
• Results in maximum number of hydrogen
atoms therefore, said to be saturated
•Tend to be straight and fit close together
• Found in animal fat and solid vegetable
shortening
•Tend to be solid at room temperature
•Example: butter and ghee

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 Triglycerides: Long-Term Energy Storage
• Unsaturated fats
• One or more double bonds between
carbons
• Results in less than maximum number of
hydrogen atoms therefore, said to be
unsaturated
• Have low melting points because the fatty
acids chains cannot closely straight
• Double bonds cause “kinks” or bends in the
chains
• Tend to be liquid at room temperature
• Example: vegetable oil
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Structure of Saturated and Unsaturated Fat

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 Triglycerides: Long-Term Energy Storage
• Cis –and Trans fats
• Un saturated fats have chemical groups on
the same (cis) or opposite (trans) side of the
double bond

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 Triglycerides: Long-Term Energy Storage

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 Synthesis and Degradation of a Triglyceride
• Three fatty acids attached to each glycerol molecule
• Carboxylic acid reacts to –OH on glycerol in dehydration
reaction one molecule of triglyceride + 3 H2O

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 Phospholipids: Membrane Components
• The structure is like 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
• The fluidity of the plasma membrane is affected by
kinks in the phospholipids’ tails

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 Phospholipids: Membrane Components
• 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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 Structure of Phospholipids

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 Steroids: Four Fused Carbon Rings
• They are composed of four fused carbon rings.
• Various functional groups attached to the C
skeleton.
• Steroids of biological importance include:
• Cholesterol - the precursor molecule for several
other steroids
• Hormones (e.g., testosterone and estrogen are sex
hormones)
• Bile salts (emulsify fats)
• Functions:
• Component of animal cell membrane, regulation
• Cholesterol can also contribute to circulatory
disorders.
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 Steroid Diversity

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 Waxes
• Waxes are ester made of long-chain fatty acids
and carbon chains containing alcohol functional
groups
• Solid at room temperature
• Waterproof
• Resistant to degradation
• Forms protective cuticle (coating) in plants
• Skin and fur maintenance in animals
• Beeswax (for honey storage)
• Earwax (contains cerumin) to repel insects and
trap dust and dirt

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 Waxes

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 3.4 Proteins
• 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.
• Two or more amino acids joined together are called
peptides.
• Long chains of amino acids joined together are
called polypeptides.
• A protein is a polypeptide that has folded into a particular
shape, which is essential for its proper function.

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 Functions of Protein
• Support
Some proteins have a structural function (e.g., keratin in nails
& hair and collagen in ligaments and tendons)
• Metabolism
Most enzymes are proteins that act as catalysts to
accelerate chemical reactions within cells
• Transport
Membrane channel and carrier proteins regulate what
substances enter and exit cells; Hemoglobin protein
transports oxygen to tissues and cells

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 Functions of Protein
• Defense
Antibodies are proteins of our immune system that bind to
antigens and destroying cells.
• Regulation
Hormones are regulatory proteins that influence the
metabolism of cells (e.g., insulin).
• Motion
Microtubules move cell components to different locations. Actin
and myosin contractile proteins allow muscles to contract.

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 Amino Acids: Protein Monomers
• There are 20 different common amino acids.
• Each amino acid has a central carbon atom.
• Two end groups
• an amino group (NH2)
• a carboxyl group (COOH)
• Amino acids differ by their R or variable groups,
which range in complexity

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 Amino Acids: Protein Monomers
• Amino acids are grouped by properties of their side
chains.
• Nonpolar side chains are hydrophobic
• Polar side chains are hydrophilic
• A side chain with a carboxyl group is acidic
• A side chain that accepts a hydrogen ion is basic
• Amino acid cysteine has an R group that ends with a – SH
(sulfide) group, which often covalently connects one chain of
amino acids to another by a disulfide bond, – S–S –.

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 Amino Acids

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 Synthesis and Degradation of a Peptide
• Dehydration reaction, a peptide bond joins two amino acids,
and a water molecule is released.
• Hydrolysis reaction, the peptide bond is broken due to the
addition of water.

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Shapes of Proteins and Levels of Protein Structure
• A protein is a poly peptide that has been folded into a
particular shape.

• Protein shape determines the function of the protein in the

organism. 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, but not all
proteins have the 4 levels.

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 Four Levels of Protein Structure
• There are four main levels of protein structure:
• Primary level – the linear sequence of amino acids that
make up the polypeptide chain.
• Secondary level – characterized by the presence of alpha
helices and beta (pleated) sheets held in place with hydrogen
bonds.
• Tertiary level – the overall three-dimensional shape of a
polypeptide formed by bending and twisting of the
polypeptide chain.
• Quaternary level – refers to the 3-D structure that results from
two or more polypeptide chains interactions.

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Copyright © McGraw-Hill Education
 Primary Structure
• Primary Structure is a linear sequence of amino acids
joined by peptide bonds and give a simple polypeptide
chain.
• Just as English alphabet contains 26 letters, 20 amino
acids can join to form a huge variety of “words.”
• Each protein has a unique sequence of amino acids.
• Changing the sequence of amino acids can produce
different proteins.
• The primary shape is the newly synthesized proteins and need to be
modified to be active and functional

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 Secondary Structure
• Secondary Structure results when a polypeptide of a
primary shape coils or folds in a particular way.
• 2 patterns of secondary structures:
• α -helix (helical coil) was the first pattern discovered
• β -pleated sheet was the second pattern discovered
• Both types may occur in the same polypeptide chain
• Fibrous proteins are either mostly alpha helices or beta
pleated sheets that hydrogen bond occurs between the –
Co of one amino acids and the –NH of another amino acid.

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 Secondary Structure
• α (alpha) Helix
• Hydrogen bonds form between
every fourth amino acid
• Basic structural unit of fibrous,
elastic proteins (e.g., hair and
animal horn)
• β (beta) Pleated Sheet
• Chain folded back with regions
of chain parallel to itself
• Spider silk and silkworm silk are
mostly β pleated sheets

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 Tertiary Structure

• Tertiary structure results when proteins of

secondary structure are folded, that results in the
final three- dimensional shape of polypeptide.
• Also called “Globular proteins” because they tend to
ball up into rounded shapes.
• Various types of bonding between R groups of the
constituent amino acids: strong disulfide linkages
maintain the tertiary shape; hydrogen, ionic, and
covalent bonds also contribute to the tertiary
structure of protein.

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 Tertiary Structure

• Hydrophobic R groups also found in the

tertiary structure. These nonpolar amino
acids tend to group together in the interior of
a protein, to be far away from water as
possible.

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 Quaternary Structure

• Quaternary structure is 3-D structure

resulting from two or more polypeptide
chains interacting in specific ways to form a
biologically active molecule.
• Hemoglobin is globular protein with a
quaternary structure of 4 polypeptide
chains. Each polypeptide in hemoglobin has
4 levels of structures: primary, secondary,
tertiary and quaternary.

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 Quaternary Structure

• Hemoglobin consists of 4 polypeptide chains

(2 alpha chains + 2 beta chains) with a
central heme (iron) unit.
• Collagen consists of 3 helical polypeptide
chains.

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 3.5 Nucleic Acids
• Nucleic acids are polymers of repeating subunits called
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)
• Perform 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 N-containing (nitrogenous) base
• 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
• Sugar of one connected to the phosphate of the next

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 Nitrogenous Bases

• Nitrogenous base may be either a double-ring purine

or a single-ring pyrimidine
• DNA contains four nitrogenous bases:
• Two purines: adenine (A) and guanine (G)
• Two pyrimidines: cytosine (C) and thymine (T)
• RNA contains the purines adenine and guanine, and
the pyrimidines cytosine and uracil (U)

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 Nucleotides

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 DNA and RNA Structure
• RNA is predominately a single-stranded molecule, whereas
DNA is a double-stranded molecule.
• Complementary base pairing occurs where two
strands of DNA are held together by hydrogen bonds
between purine and pyrimidine bases.
• In DNA, thymine is always paired with adenine; cytosine is
always paired with guanine.
• The number of A + G (purine bases) always equals the
number of C + T (pyrimidine bases).
• Two strands of DNA twist to form a double helix; RNA does not
form helices.

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 DNA Structure

DNA is double helix in which the two polynucleotide strands twist about
each other. Hydrogen bonds occur between the complementary paired
bases. C is always paired with G, and A is always paired with T.

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 RNA Structure

RNA is single-stranded polymer of nucleotides. When Nucleotides join, the

phosphate group of one is bonded to the sugar of the next. The nitrogen
bases project out to the side of the resulting sugar-phosphate backbone.

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 DNA Structure Compared to RNA
Structure

DNA RNA

Sugar Deoxyribose Ribose

Adenine, guanine, Adenine, guanine, uracil,

Bases
thymine, cytosine
cytosine
Strands Double stranded
Single stranded
with base pairing

Helix Yes No

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 ATP (Adenosine Triphosphate)
• ATP 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
• ATP is called the energy currency of the cell.
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 ATP (Adenosine Triphosphate)
• 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, muscle contraction and
nerve impulse conduction.

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