Biology

Sylvia S. Mader
Michael Windelspecht

Chapter 3
The Chemistry of
Organic Molecules
Lecture Outline

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1
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 3.1 Organic Molecules
• Organic molecules contain carbon and
hydrogen atoms.

• Four classes of organic molecules

(biomolecules) exist in living organisms:
 Carbohydrates
 Lipids
 Proteins
 Nucleic Acids

2
Inorganic versus Organic Molecules

3
 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

4
Table 3.2
 Isomers

• Isomers are organic molecules that have

identical molecular formulas but a different
arrangement of atoms.
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glyceraldehyde dihydroxyacetone

H H O H O H

H C C C H H C C C H

OH OH OH OH

6
 Biomolecules
• 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)

7
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Fig. 3.3

Biomolecules

Category Subunit(s) Polymer

Carbohydrates* Monosaccharide Polysaccharide

Lipids Glycerol and fatty acids Fat

Proteins* Amino acids Polypeptide

Nucleic acids* Nucleotide DNA,RNA

*Polymers
© The McGraw Hill Companies, Inc./John Thoeming, photographer
 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 breakdown polymers into monomers
 Example: digestion of starch into glucose monomers

9
Synthesis and Degradation of Biomolecules

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monomer OH
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monomer OH +
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monomer OH + H monomer
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monomer OH + H monomer

H2O
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monomer OH + H monomer

Dehydration H 2O
reaction

monomer monomer

a. Synthesis of a biomolecule
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monomer monomer
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H 2O

monomer monomer
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Dehydration H2O
reaction

monomer monomer
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monomer OH H monomer

Hydrolysis
reaction H 2O

monomer monomer

b. Degradation of a biomolecule
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monomer OH H monomer

dehydration H2O
reaction

monomer monomer

a. Synthesis of a biomolecule

monomer OH H monomer

hydration
reaction H2O

monomer monomer

b. Degradation of a biomolecule
 Synthesis and Degradation

• 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.

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 3.2 Carbohydrates
• Functions:
 Energy source
 Provide building material (structural role)

• Contain carbon, hydrogen and oxygen in a 1:2:1

ratio

• Varieties: monosaccharides, disaccharides, and

polysaccharides
 Monosaccharides

• A monosaccharide is a single sugar molecule.

• Also called simple sugars
• Have a backbone of 3 to 7 carbon atoms
• Examples:
 Glucose (blood), fructose (fruit) and galactose
• Hexoses - six carbon atoms
 Ribose and deoxyribose (in nucleotides)
• Pentoses – five carbon atoms

22
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Glucose
Fig. 3.6

CH2OH CH2OH
6
C O O
H 5 H H H
H H
C C
4 OH H 1 OH H
HO C OH HO OH
C
a. 3 2 b.
H OH H OH

C6H12O6

O O

c. d.
© Steve Bloom/Taxi/Getty
 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.
24
Synthesis and Degradation of Maltose

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CH2OH CH2OH
O H H O

+
OH HO

glucose C6H12O6 glucose C6H12O6

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CH2OH CH2OH
O O
H H dehydration reaction
+
OH HO

glucose C6H12O6 glucose C6H12O6

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CH2OH CH2OH CH2OH CH2OH

O O O O
H H dehydration reaction
+ O + H2O
OH HO

glucose C6H12O6 glucose C6H12O6 maltose C12H22O11 water

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CH2OH CH2OH CH2OH CH2OH

O O O O
H H dehydration reaction
+ O + H2O
OH HO

glucose C6H12O6 glucose C6H12O6 maltose C12H22O11 water

monosaccharide + monosaccharide disaccharide + water

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CH2OH CH2OH
O O

maltose C12H22O11
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CH2OH CH2OH
O O

O + H2O

maltose C12H22O11 water

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CH2OH CH2OH
O O

O + H2O
hydrolysis reaction

maltose C12H22O11 water

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CH2OH CH2OH CH2OH CH2OH

O O O O
H H

+ O + H2O
OH HO hydrolysis reaction

glucose C6H12O6 glucose C6H12O6 maltose C12H22O11 water

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CH2OH CH2OH CH2OH CH2OH

O O O O
H H

+ O + H2O
OH HO hydrolysisreaction

glucose C6H12O6 glucose C6H12O6 maltose C12H22O11 water

monosaccharide + monosaccharide disaccharide + water

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dehydration reaction

hydrolysis reaction

glucose C6H12O6 glucose C6H12O6 maltose C12H22O11 water

monosaccharide + monosaccharide disaccharide + water

 Polysaccharides

• 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.
 Chitin is found in the cell walls of fungi and
exoskeleton of some animals.
 Peptidoglycan is found in the cell walls of bacteria.
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Amylose:
nonbranched

starch
granule

Amylopectin:
branched

a. Starch 250 m

glycogen
granule

b . Glycogen 150 nm

a: © Jeremy Burgess/SPL/Photo Researchers, Inc.; b: © Don W. Fawcett/Photo Researchers, Inc.

 3.3 Lipids
• Lipids are varied in structure.
• Large nonpolar molecules that are insoluble in water
• Functions:
 Long-term energy storage
 Structural components
 Cell communication and regulation
 Protection

• Varieties: fats, oils, phospholipids, steroids, waxes

 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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H C OH

H C OH

H C OH

glycerol
a. Formation of a fat
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H H H H H
H O
C C C C C C H
H C OH HO
H H H H H

H H H H H H H
O
+ C C C C C C C C H
H C OH HO
H H H H H H H

H H H
O H
H
C C C C C
H C OH HO C
H H H
H H
in

glycerol 3 fatty acids

a. Formation of a fat
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H H H H H
H O 3 H2 O
C C C C C C H
H C OH HO
H H H H H

H H H H H H H
O
+ C C C C C C C C H
H C OH HO
H H H H H H H

H H H
O H
H
C C C C C 3 H2 O
H C OH HO C
H H H
H H
in

glycerol 3 fatty acids 3 water

a. Formation of a fat molecules
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H H H H H H H O H H H H H
O 3 H2O
C C C C C C H H C O C C C C C C H
H C OH HO
H H H H H H H H H H

H H H H H H H O H H H H H H H
O

H C OH
+ C C C C C C C C H H C H C C C C C C C C H
HO
H H H H H H H H H H H H H H

H H H O H H H
O H H
H O H
C C C C 3 H2O H C C C C C
C C
H C OH HO C C
H H H H H H H
H H H
in in

glycerol 3 fatty acids 3 water fat molecule

a. Formation of a fat molecules
Triglycerides: Long-Term Energy Storage
• Fatty acids are either unsaturated or saturated.
 Unsaturated - one or more double bonds between
carbons
• Tend to be liquid at room temperature
– Example: plant oils

 Saturated - no double bonds between carbons

• Tend to be solid at room temperature
– Examples: butter, lard

44
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H H H H H H H O H H H H H
O 3 H2O
C C C C C C H H C O C C C C C C H

Fig. 3.10
H C OH HO
H H H H H H H H H H

H H H H H H H O H H H H H H H
O
+ C C C C C C C C H H C H C C C C C C C C H
H C OH HO
H H H H H H H H H H H H H H

H H H O H H H
O H H
C C C C H H C O C C C C H
C 3 H2O C
H C OH HO C C
H H H H H H H
H H H
in in

glycerol 3 fatty acids 3 water fat molecule

molecules
a. Formation of a fat

corn corn oil

H H H H H H H H H H H H H H H
O
C C C C C C C C C C C C C C C C C C H
HO
H H H H H H H H H H H H H

unsaturated fatty acid with double bonds (yellow)

unsaturated fat

mil butter

H H H H H H H H H H H H H H H
O
C C C C C C C C C C C C C C C C H
HO
H H H H H H H H H H H H H H H

saturated fatty acid with no double bonds saturated fat

b. Types of fatty acids c. Types of fats
 Phospholipids: Membrane Components
• Structure is similar to triglycerides
 Consist of one glycerol molecule linked to two fatty
acids and a modified phosphate group
• The fatty acids are nonpolar and hydrophobic.
• The modified phosphate group is polar and
hydrophilic.
• Function: form plasma membranes
• In water, phospholipids aggregate to form a lipid
bilayer.
 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.
46
Phospholipids Form Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Membranes
glycerol
O
Fig. 3.11CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH
CH2 CH2 2 CH2 CH3
Polar 1
CH2 O
C CH2

Head 2
fatty acids
O CH2 O

R O P O CH2
3 C CH2 CH
2 CH2 CH
2 CH2 CH2 CH2 CH CH
CH
O 2
CH
Nonpolar Tails 2
CH
phosphate 2
CH
2
CH
a. Phospholipid structure 2
CH
2
CH
2
CH
3

outside cell
inside cell

b.. Plasma membrane of a cell

 Steroids: Four Fused Carbon Rings

• 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
• Cholesterol is the precursor molecule for
several other steroids.

48
 Steroid Diversity
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OH
CH3

CH3

O
b. Testosterone

CH3

HC CH3

(CH2)3
OH
HC CH3 CH3
CH3

CH3

HO

HO c. Estrogen
a. Cholesterol
© Ernest A. Janes/Bruce Coleman/Photoshot
 Waxes
• Long-chain fatty acid bonded to a long-chain
alcohol
• Solid at room temperature
• Waterproof
• Resistant to degradation
• Function: protection
• Examples: earwax, plant cuticle, beeswax

50
 Waxes

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a. b.

a: © Das Fotoarchiv/Peter Arnold, Inc.; b: © Martha Cooper/Peter Arnold, Inc.

51
 3.4 Proteins
• Proteins are polymers of amino acids linked
together by peptide bonds.
 A peptide bond is a covalent bond between amino
acids.

• 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 and has function.

52
 Functions of Proteins
• Metabolism
 Most enzymes are proteins that act as catalysts to accelerate
chemical reactions within cells.
• Support
 Keratin and collagen

• Transport
 Hemoglobin and membrane proteins

• Defense
 Antibodies

• Regulation
 Hormones are regulatory proteins that influence the metabolism of
cells.
• Motion
 Muscle proteins and microtubules
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 Amino Acids: Protein Monomers
• There are 20 different common amino acids.
• Amino acids differ by their R groups.
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amino acidic
group group
H

H2N C COOH

R
R = rest of molecule
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Sample Amino Acids with Nonpolar (Hydrophobic) R Groups

H O H H O
O
H H3N+ C C H3N + C C H3N+ C C H
O O
O O
H3N+
CH2 O CH2 H2N +
C C
C C (CH2)2
O
O CH H2C CH2
CH S
CH3 CH3 CH3 CH2
H3C CH3
valine (Val) methionine (Met) phenylalanine (Phe) leucine (Leu) proline (Pro)

Sample Amino Acids with Polar (Hydrophilic) R Groups

H O H O H O H O
H3N+ C C H3N+ C C H3N+ C C H3N+ C C
O O O (CH2)2 O
CH2 CH CH2
SH OH C
cysteine (Cys) serine (Ser)
H O NH2 O
H3N+ C H OH glutamine (Gln)
C O
tyrosine (Tyr)
O H3N+ C C
CH2
CH O
C
NH2 O OH CH3
asparagine (Asn) threonine (Thr)

Sample Amino Acids with Ionized R Groups

H O H O
H O H3N +
C C H3N + C C H O
H O
H3N C O (CH2)3 O C
+
C CH2 H3N+ C H3N+ C
C
O CH2 O
CH2 CH2 O NH
CH2
CH2 NH
CH2 C C N+H2
COO- N+H3 OO NH2 N+H
glutamicacid (Glu) lysine (Lys) aspartic acid (Asp) arginine (Arg) histidine (His)
Synthesis and Degradation of a Peptide
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amino group

amino acid
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amino group acidic group

amino acid amino acid

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amino group acidic group

dehydration reaction

amino acid amino acid

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amino group acidic group peptide bond

dehydration reaction

amino acid amino acid water

dipeptide
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amino group acidic group peptide bond

dehydration reaction

hydrolysis reaction

amino acid amino acid water

dipeptide
 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

61
 Four Levels of Protein Structure
 Primary
• The sequence of amino acids
 Secondary
• Characterized by the presence of alpha helices and
beta (pleated) sheets held in place with hydrogen
bonds
 Tertiary
• Final overall three-dimensional shape of a
polypeptide
• Stabilized by the presence of hydrophobic
interactions, hydrogen bonding, ionic bonding, and
covalent bonding
 Quaternary
• Consists of more than one polypeptide 62
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H3N+

Primary Structure
This level of structure amino acid
is determined by the peptide bond COO–
sequence of amino
acids coded by a
gene that joins to
form a polypeptide.

C
O
CH C hydrogen bond
O C N O
R C C
CH
C H N H C
N R hydrogen bond R C O H O
CH O C C
H R C
R C C N
O H R C H
O N H N
CH N
C N R H C
C R C O O
CH O O H
C C N
N R H R
O C N H N C
H H O R
Secondary Structure CH R C O C
C
O C N R C
Hydrogen bonding CH R C N
O H R C
between amino acids C H N
N N
R
causes the polypeptide CH C
C O
to form an alpha helix O H
or a pleated sheet. N
α alpha) helix Β (beta) sheet = 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 disulfide bond
of a protein.
Quaternary Structure

This level of structure

occurs when two or more
folded polypeptides interact
to perform a biological function.
 Examples of Fibrous Proteins

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a. b. c.
a: © Gregory Pace/Corbis; b: © Ronald Siemoneit/Corbis Sygma; c: © Kjell Sandved/Visuals Unlimited

64
 Protein-Folding Diseases

• Chaperone proteins help proteins fold into their

normal shape.
 Defects in chaperone proteins may play a role in
several human diseases such as Alzheimer 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 disease.

65
 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

66
 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.

67
 Nucleotides
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phosphate nitrogen-
P C containing
base
5' O

4' S 1'
3' 2'
pentose sugar
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O
nitrogen-
phosphate P C containing
–
O P O
base
O– 5' O

4' S 1'
3' 2'
pentose sugar
a. Nucleotide structure
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O
nitrogen- CH2OH
phosphate P C containing
–
O P O OH
base O
O– O C H H C
5'

S H C C H
4' 1'

3' 2' OH H
pentose sugar deoxyribose (in DNA)
a. Nucleotide structure b. Deoxyribose versus ribose
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O
nitrogen- CH2OH CH2OH
phosphate P C containing
–O P O OH OH
base O O
O– O C H H C C H H C
5'

S H C C H H C C H
4' 1'

3' 2' OH H OH OH
pentose sugar deoxyribose (in DNA) ribose (in RNA)
a. Nucleotide structure b. Deoxyribose versus ribose
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Pyrimidines Purines
NH2 O O
NH2 O
C C CH3 C
N CH HN C CH C N C N
HN N C C
C T U HN
CH CH C CH A CH G CH
HC C C
O N O N O N N N
H H H N H2N N H
H
cytosine thymine in DNA uracil in RNA adenine guanine
c. Pyrimidines versus purines
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O
nitrogen- CH2OH CH2OH
phosphate P C containing
–O P O OH OH
base O O
O– O C H H C C H H C
5'

S H C C H H C C H
4' 1'

3' 2' OH H OH OH
pentose sugar deoxyribose (in DNA) ribose (in RNA)
a. Nucleotide structure b. Deoxyribose versus ribose

Pyrimidines Purines
NH2 O O
NH2 O
C C CH3 C
N CH HN C CH C N C N
HN C C
C T U N HN
CH CH C CH A CH G CH
HC C
O N O N N N C N
O N H2N N
H H H H H
cytosine thymine in DNA uracil in RNA adenine guanine
c. Pyrimidines versus purines
 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.
 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 to
form a double helix.
– Adenine hydrogen bonds with thymine
– Cytosine hydrogen bonds with guanine
• The bonding between the nucleotides in DNA is
referred to as complementary base pairing.

74
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Fig. 3.19
RNA Structure
N O
N
G N
P
N
NH2
S
H Nitrogen-containing
bases
O N 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
T A

C G

A T

G C

C CCytosine S Sugar
G GGuanine A AAdenine
P Phosphate T TThymine

a. Space-filling model b. Double helix

H
―

Complementary
―
N H O

―
―

N H
― N
N
N
―

N sugar
―

―
Base Pairing in ―
O
―
sugar H N H

cytosine (C) guanine (G)

DNA H
― ―

―
N N H O CH3
―

C
N
N H N
sugar N N
―
―

O
sugar
adenine (A) thymine (T)
c. Complementary base pairing

© Photodisk Red/Getty RF
 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.

78
 ATP
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a. adenosine triphosphate c.

NH2 NH2

N N H2O N N

N N P P P N N P P + P + ENERGY

adenosine triphosphate adenosine diphosphate phosphate

b. ATP ADP
c: © Jennifer Loomis / Animals Animals / Earth Scenes