Biology

Sylvia S. Mader
Michael Windelspecht

Chapter 3
The Chemistry of Organic
Molecules
Lecture Outline
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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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 Trans-Fats and Cardiovascular
Health
• Trans-fats (a type of fat, or lipid)
 Are made by adding hydrogen to unsaturated fats, a
process called hydrogenation.
 Are used to increase food shelf life and flavor/texture.
 May cause worse health effects than saturated fat in an
individual’s diet.
• FDA now requires trans-fat labeling on foods and in
restaurants.

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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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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 at any carbon make carbon chains more
complex.
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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
 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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 Isomers

• Isomers are organic molecules that have

identical molecular for mulas but different
arrangements of atoms.
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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.

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 The Biomolecules of Cells-1

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Table 3.2 Biomolecules

Category 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 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

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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
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Synthesis and Degradation of Biomolecules-5

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Synthesis and Degradation of Biomolecules-6

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Synthesis and Degradation of Biomolecules-7
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Synthesis and Degradation of Biomolecules-8
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Synthesis and Degradation of Biomolecules-9
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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

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 3.2 Carbohydrates
• 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 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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Glucose

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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
lactose which breaks down lactose into galactose
and glucose.
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Synthesis and Degradation of Maltose

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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

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Synthesis and Degradation of Maltose-4
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Synthesis and Degradation of Maltose-5
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Synthesis and Degradation of Maltose-6

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Synthesis and Degradation of Maltose-7

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Synthesis and Degradation of Maltose-8

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Synthesis and Degradation of Maltose-9

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 Polysaccharides: Energy-Storage and
Structural Molecules
• 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
exoskeleton of some animals.
 Peptidoglycan is found in the cell walls of
bacteria.
 Monomers contain an amino acid chain. 38
Polysaccharides: Energy-Storage and
Structural Molecules-1
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3.7a: © Jeremy Burgess/SPL/Science Source; 3.7b: © Don W. Fawcett/Science Source 39
Polysaccharides: Energy-Storage and
Structural Molecules-2

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 3.3 Lipids
• 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-1
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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
 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-1
• 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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Triglycerides: Long-Term Energy Storage-2

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Triglycerides: Long-Term Energy Storage-3

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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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 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
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Phospholipids Form Membranes

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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.
• Cholesterol is the precursor molecule for several
other steroids.
• Cholesterol can also contribute to circulatory
disorders.
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 Steroid Diversity
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© Ernest A. Janes/Bruce Coleman/Photoshot

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 Waxes
• 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 cerumin), plant
cuticle, beeswax

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Waxes-1

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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.
 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.

• A protein is a polypeptide that has folded into

a particular shape, which is essential for its
proper functioning.
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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.

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 Amino Acids: Protein Monomers
• 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-1

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Synthesis and Degradation of a Peptide
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Synthesis and Degradation of a Peptide-1

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Synthesis and Degradation of a Peptide-2

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Synthesis and Degradation of a Peptide-3

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Synthesis and Degradation of a Peptide-4

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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
 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.
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Four Levels of Protein Structure-1

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Examples of Fibrous Proteins

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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 misfold. 69
 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)
• 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 nitrogen-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, which is a sequence of
nucleotides.

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 Nucleotides
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 Nucleotides-1
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 Nucleotides-2

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 Nucleotides-3

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 Nucleotides-4

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 Nucleotides-5
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 Structure of DNA and RNA
 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 to 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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 Structure of DNA and RNA-1
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Table 3.4 DNA Structure Compared to RNA Structure

DNA RNA
Sugar Deoxyribose Ribose

Bases Adenine, guanine, Adenine, guanine, uracil,

thymine, cytosine cytosine
Strands Double stranded with Single stranded
base pairing
Helix Yes No

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RNA Structure

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DNA Structure

Complementary
Base Pairing in
DNA
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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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ATP

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Appendix : Long Description for
Visuals

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 Long Description for Inorganic versus
Organic Molecules-1

Carbon and life. Carbon is the basis of life as we know it. The structure of carbon allows for the
formation of (a) the lipids that store energy in this canola plant; (b) carbohydrates that provide
structure for this tree; (c) the proteins that form the hemoglobin of red blood cells; and (d) the
genetic material that allows this lioness to pass on information to her offspring.

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 Long Description for Isomers

Isomers. Isomers have the same molecular formula but different atomic configurations. Both of
these compounds have the formula C3H6O3. In glyceraldehyde, a colorless crystalline solid,
oxygen is double-bonded to an end carbon. In dihydroxyacetone, a white crystalline solid, oxygen
is double-bonded to the middle carbon.

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Long Description for Synthesis and Degradation
of Biomolecules-9

Synthesis and degradation of biomolecules. a. In cells, synthesis often occurs when subunits
bond during a dehydration reaction (removal of H2O). b. Degradation occurs when the subunits
separate during a hydrolysis reaction (the addition of H2O).

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Long Description for Synthesis and Degradation-2

Carbohydrates as structural materials. a. Plants, such as the cactus shown here, have the
carbohydrate cellulose in their cell walls. b. The shell of a crab contains a carbohydrate called
chitin. c. The cell walls of bacteria contain a carbohydrate known as peptidoglycan.

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 Long Description for Glucose

Glucose. Glucose is the common form of monosaccharide that provides energy for cells. Each of
these structural formulas is glucose. a. The carbon skeleton and all attached groups are shown.
b. The carbon skeleton is omitted. c. The carbon skeleton and attached groups are omitted. d.
Only the ring shape, which includes one oxygen atom, remains.

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Long Description for Synthesis and Degradation
of Maltose-9

Synthesis and degradation of maltose, a disaccharide. Synthesis of maltose occurs following a

dehydration reaction when a bond forms between two glucose molecules, and water is removed.
Degradation of maltose occurs following a hydrolysis reaction when this bond is broken by the
addition of water.

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Long Description for Polysaccharides: Energy-
Storage and Structural Molecules-1

Starch and glycogen structure and function. a. The electron micrograph shows the location of
starch in plant cells. Starch is a chain of glucose molecules that can be branched or unbranched.
b. The electron micrograph shows glycogen deposits in a portion of a liver cell. Glycogen is a
highly branched polymer of glucose molecules.

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Long Description for Polysaccharides: Energy-
Storage and Structural Molecules-2

Cellulose fibrils. Cellulose fibers crisscross in plant cell walls for added strength. A cellulose fiber
contains several microfibrils, each a polymer of glucose molecules—notice that the linkage bonds
differ from those of starch. Every other glucose is flipped, permitting hydrogen bonding and
greater strength between the microfibrils.

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Long Description for Triglycerides: Long-Term
Energy Storage-2

Saturated and unsaturated fatty acids. A fatty acid has a carboxyl group attached to a long
hydrocarbon chain. a. If there are no double bonds between the carbons in the chain, the fatty
acid is saturated. b. If there are double bonds between some of the carbons, the fatty acid is
unsaturated and a kink occurs in the chain.

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Long Description for Triglycerides: Long-Term
Energy Storage-6

Synthesis and degradation of a triglyceride. Following a dehydration reaction, glycerol is bonded

to three fatty acid molecules as fat forms and water is given off. Following a hydrolysis reaction,
the bonds are broken due to the addition of water.

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 Long Description for Phospholipids Form
Membranes

Phospholipids form membranes. a. Phospholipids are constructed like fats, except that in place of
the third fatty acid, they have a polar phosphate group. The hydrophilic (polar) head is soluble in
water, whereas the two hydrophobic (nonpolar) tails are not. A tail has a kink wherever there is an
unsaturated bond. b. Because of their structure, phospholipids form a bilayer that serves as the
major component of a cell’s plasma membrane. The fluidity of the plasma membrane is affected
by kinks in the phospholipids’ tails.

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 Long Description for Steroid Diversity

Steroid diversity. a. Built like cholesterol, (b) testosterone and (c) estrogen have different effects
on the body due to different functional groups attached to the same carbon skeleton. Testosterone
is the male sex hormone active in peacocks (left), and estrogen is the female sex hormone active
in peahens (right). These hormones are present in many living creatures.

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 Long Description for Waxes-1

Waxes. Waxes are a type of lipid. a. Fruits are protected by a waxy coating, which is visible on
these plums. b. Bees secrete the wax that allows them to build a comb, where they store honey.

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 Long Description for Amino Acids: Protein
Monomers-1

Amino acids. Polypeptides contain 20 different kinds of amino acids, some of which are shown
here. Amino acids differ by the particular R group (shaded area of the molecule) attached to the
central carbon. Some R groups are nonpolar and hydrophobic (top), some are polar and
hydrophilic (center), and some are ionized and hydrophilic (bottom). The amino acids are shown
in ionized form.

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Long Description for Synthesis and Degradation
of a Peptide-4

Synthesis and degradation of a peptide. Following a dehydration reaction, a peptide bond joins
two amino acids and a water molecule is released. Following a hydrolysis reaction, the bond is
broken due to the addition of water.

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 Long Description for Four Levels of Protein
Structure-1

Levels of protein organization. All proteins have a primary structure. Both fibrous and globular
proteins have a secondary structure; they are either helices (keratin, collagen) or pleated sheets
(silk). Globular proteins always have a tertiary structure, and most have a quaternary structure
(e.g., hemoglobin and enzymes such as RNase).

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 Long Description for Examples of Fibrous
Proteins

Fibrous proteins. Fibrous proteins are structural proteins. a. Keratin—found, for example, in hair,
horns, and hooves—exemplifies fibrous proteins that are helical for most of their length. b. A
chemical treatment, called a perm, may be used to alter the secondary structure of the keratin
proteins. c. Silk made by spiders is fibrous proteins that are pleated sheets for most of their
length. Hydrogen bonding between parts of the molecule causes the pleated sheet to double back
on itself.

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 Long Description for Nucleotides-5

Nucleotides. a. A nucleotide consists of a pentose sugar, a phosphate molecule, and a nitrogen-

containing base. b. DNA contains the sugar deoxyribose, and RNA contains the sugar ribose. c.
DNA contains the pyrimidines C and T and the purines A and G. RNA contains the pyrimidines C
and U and the purines A and G.

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 Long Description for RNA Structure

RNA structure. RNA is a single-stranded polymer of nucleotides. When the nucleotides join, the
phosphate group of one is bonded to the sugar of the next. The bases project out to the side of
the resulting sugar–phosphate backbone.

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 Long Description for DNA Structure

DNA structure. a. Space-filling model of DNA. b. DNA is a double helix in which the two
polynucleotide strands twist about each other. c. Hydrogen bonds (dotted lines) occur between
the complementarily paired bases: C is always paired with G, and A is always paired with T.

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 Long Description for ATP

ATP. ATP, the universal energy currency of cells, is composed of adenosine and three phosphate
groups. a. Space-filling model of ATP. b. When cells require energy, ATP becomes ADP + , and
energy is released.

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