Chapter 3: pp. 37-58
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10th Edition
Sylvia S. Mader
The Chemistry of
Organic Molecules
BIOLOGY
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PowerPoint® Lecture Slides are prepared by Dr. Isaac Barjis, Biology Instructor
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1
Outline

Organic vs Inorganic

Functional Groups and Isomers

Macromolecules

Carbohydrates

Lipids

Proteins

Nucleic Acids
2
Organic Molecules



Organic molecules contain carbon and
hydrogen atoms bonded to other atoms
Organic molecules are a diverse group
Four types of organic molecules
(biomolecules) exist in organisms:




Carbohydrates
Lipids
Proteins
Nucleic Acids
3
Organic versus Inorganic Molecules
4
Carbohydrates as Structural Materials
Plants cell wall
consist of
cellulose
 Cell wall of fungi
and shell of crab
contain chitin
 Bacterial cell wall
contain
peptidoglycan

Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
b. Shell contains chitin.
a. Cell walls contain cellulose.
c. Cell walls contain peptidoglycan.
a: © Brand X Pictures/PunchStock; b: © Ingram Publishing/Alamy; c: © H. Pol/CNRI/SPL/Photo
Researchers, Inc.
5
Carbon Atom


Carbon atoms:

Contain a total of 6 electrons

Only four electrons in the outer shell

Very diverse as one atom can bond with up to four
other atoms
Often bonds with other carbon atoms to make
hydrocarbons

Can produce long carbon chains like octane

Can produce ring forms like cyclohexane
6
Octane & Cyclohexane
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octane
cyclohexane
7
Functional Groups

Functional groups are clusters of specific atoms bonded
to the carbon skeleton with characteristic structure and
functions

Always react in the same manner, regardless of where attached

Determine activity and polarity of large organic molecules

Many functional groups, but only a few are of major
biological importance

Depending on its functional groups, an organic molecule
may be both acidic and hydrophilic

Nonpolar organic molecules are hydrophobic (cannot
dissolve in water) unless they contain a polar functional
group
8
Biologically Important Functional Groups
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Functional Groups
Group
Hydroxyl
Structure
R
OH
Compound
Alcohol
as in
ethanol
Significance
Polar, forms
hydrogen bond
Present in sugars,
some amino acids
O
Carbonyl
R
C
H
O
Carboxyl
(acidic)
R
C
R
C
R
O
OH
Amino
R
H
N
Aldehyde
as in
formaldehyde
Polar
Ketone
as in
acetone
Polar
Carboxylic acid
as in
acetic acid
Polar, acidic
Present in sugars
Present in sugars
Present in fatty
acids, amino acids
Amine
Polar, basic, forms
as in tryptophan hydrogen bonds
H
Present in amino acids
Sulfhydryl
Phosphate
R
SH
O
R O P OH
OH
Thiol
Forms disulfide bonds
as in ethanethiol
Present in some
amino acids
Organic
phosphate
as in
phosphorylated
molecules
Polar, acidic
Present in
nucleotides,
phospholipids
R = remainder of molecule
9
Isomers

Isomers - organic molecules that have:
Identical molecular formulas, but
 Differing internal arrangement of atoms

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glyceraldehyde
H
H
H
O
C
C
C
OH OH
H
dihydroxyacetone
H
H
O
H
C
C
C
OH
H
OH
10
Macromolecules

Carbohydrates, lipids, proteins, and nucleic
acids are called macromolecules because of
their large size.

Usually consist of many repeating units




Resulting molecule is a polymer (many parts)
Repeating units are called monomers
E.g. amino acids (monomer) are linked to form a protein
(polymer)
Some examples:
Category
Example
Subunit(s)
Lipids
Fat
Glycerol & fatty acids
Carbohydrates Polysaccharide Monosaccharide
Proteins
Polypeptide
Nucleic Acids DNA, RNA
Amino acid
Nucleotide
11
Common Foods
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12
Animation
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Dehydration and Hydrolysis

Dehydration - Removal of water molecule



Hydrolysis - Addition of water molecule



Used to connect monomers together to make polymers
Polymerization of glucose monomers to make starch
Used to disassemble polymers into monomer parts
Digestion of starch into glucose monomers
Specific enzymes required for each reaction



Accelerate reaction
Are not used in the reaction
Are not changed by the reaction
14
Biomolecules
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Biomolecules
Category
Example
Subunit(s)
Carbohydrates*
Polysaccharide
Monosaccharide
Lipids
Fat
Glycerol and fatty acids
Proteins*
Polypeptide
Amino acids
Nucleic acids*
DNA, RNA
Nucleotide
*Polymers
15
Synthesis and Degradation of Polymers
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monomer
OH
H
dehydration
reaction
monomer
monomer
H2O
monomer
a. Synthesis of a biomolecule
monomer
OH
hydrolysis
reaction
monomer
H
monomer
H2O
monomer
b. Degradation of a biomolecule
16
Carbohydrates


Monosaccharides:

Are a single sugar molecule such as glucose, ribose, deoxyribose

Are with a backbone of 3 to 7 carbon atoms (most have 6 carbon).
Disaccharides:


Contain two monosaccharides joined by dehydration reaction

Lactose is composed of galactose and glucose and is found in milk.

Sucrose (table sugar) is composed of glucose and fructose
Polysaccharides - Are polymers of monosaccharides

Polysaccharides as Energy Storage Molecules


Starch, Glycogen
Polysaccharides as Structural Molecules

Cellulose, Chitin
17
Popular Models for Representing
Glucose Molecules
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CH2OH
O H
H
CH2OH
O H
H C
H
C
C
OH
H
HO C
C OH
a.
H
OH
H
OH
HO
b.
OH
H
OH
C6H12O6
O
c.
O
© Steve Bloom/Taxi/Getty
d.
18
Synthesis and Degradation
of Maltose, a Disaccharide
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
CH2OH
CH2OH
O
H
H
OH
+
CH2OH
O
dehydration reaction
O
O
H2O
maltose C12H22O11
water
hydrolysis reaction
HO
glucose C6H12O6
monosaccharide
CH2OH
O
glucose C6H12O6
monosaccharide
disaccharide
+
water
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
CH2OH
CH2OH
O
glucose
O
O
sucrose
fructose
CH2OH
19
Carbohydrates: Monosaccharides

Single sugar molecules

Quite soluble and sweet to taste

Examples


Glucose (blood), fructose (fruit) and galactose

Hexoses - Six carbon atoms

Isomers of C6H12O6
Ribose and deoxyribose (in nucleotides)

Pentoses – Five carbon atoms

C5H10O5 & C5H10O4
20
Carbohydrates: Disaccharides
Contain two monosaccharides joined by
dehydration reaction
 Soluble and sweet to taste
 Examples

Lactose is composed of galactose and glucose
and is found in milk
 Sucrose (table sugar) is composed of glucose
and fructose
 Maltose is composed of two glucose molecules

21
Carbohydrates: Polysaccharides

Polymers of monosaccharides
 Low solubility; not sweet to taste
 Polysaccharides as Energy Storage Molecules

Starch found in plant





Polymer of glucose
Few side branches
Used for short-term energy storage
Amylose and amylopectin are the two forms of starch found in
plants
Glycogen is the storage form of glucose in animals.


Highly branched polymer of glucose with many side branches
Glycogen in liver and muscles
22
Carbohydrates: Polysaccharides

Polysaccharides as Structural Molecules

Cellulose is a polymer of glucose which forms
microfibrils
Primary constituent of plant cell walls
 Main component of wood and many natural fibers
 Indigestible by most animals


Chitin is a polymer of glucose with an amino
group attached to each glucose
Very resistant to wear and digestion
 Primary constituent of arthropod exoskeletons (e.g.
Crab) and cell walls of fungi

23
Starch Structure and Function
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starch
granule
a. Starch
250mm
© Jeremy Burgess/SPL/Photo Researchers, Inc.
24
Glycogen Structure and Function
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
glycogen
granule
150 nm
b . Glycogen
© Don W. Fawcett/Photo Researchers, Inc.
25
Cellulose Structure and Function
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
cellulose fiber
microfibrils
Plant
cell wall
cellulose fibers
5,000 m
glucose molecules
© Science Source/J.D. Litvay/Visuals Unlimited
26
Lipids

Lipids are varied in structure

Insoluble in water



Long chains of repeating CH2 units
Renders molecule nonpolar
Lack polar groups
27
Lipids

Fat provides insulation
and energy storage in
animals
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© Paul Nicklen/National Geographic/Getty
28
Types of Lipids
29
Types of Lipids: Triglycerides


Fats and oils contain two molecular units:
glycerol and fatty acids.
Dehydration Synthesis of Triglyceride from
Glycerol and Three Fatty Acids
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H
H C
H C
O
OH
OH
H
H
H
H
H
C
C
C
C
H C
H
H
H
H
H
H
H
H
H
H
C C
C
C
C
C
C
C
HO
+
HO
C
OH
H
glycerol
a. Formation of a fat
dehydration reaction
O
O
H C
H
HO
H
H
H
H
C
C
H
H
H
H
H
H C
kink
3 fatty acids
O
O
H
H
H
H
C
C
C
C
C
H
H
H
H
O
H
H
H
H
H
H
C
C
C
C
C
C
C
H
H
H
H
H
H
O H
H
H
H
+ 3 HO
2
hydrolysis reaction
H C
H
H
O
O
C
C
C
H
kink
fat molecule
3 water
molecules
30
Types of Lipids: Triglycerides
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
corn
corn oil
H
H
H
H
H
H
H
C
C
C
C
C
C
C
C
H
H
H
H
H
H
H
H
H
H
C
C
C
H
H
H
H
C
C
C
H
H
H
H
H
C
C
C
H
H
O
C
HO
H
unsaturated fatty acid with double bonds (yellow)
unsaturated fat
milk
butter
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
C C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
C
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
O
HO
saturated fatty acid with no double bonds
b. Types of fatty acids
H
saturated fat
c. Types of fats
31
Types of Lipids: Triglycerides

Triglycerides (Fats)


Long-term energy storage
Consist of a backbone of one glycerol molecule


Glycerol is a water-soluble compound with three hydroxyl
groups.
Three fatty acids attached to each glycerol molecule

Long hydrocarbon chain




Saturated - no double bonds between carbons e.g. in fats
(butter)
Unsaturated - 1 or more than1 double bonds between carbons
e.g. in oils
Carboxylic acid at one end
Carboxylic acid connects to –OH on glycerol in dehydration
reaction
32
Types of Lipids: Phospholipids

Phospholipids
 Derived from triglycerides



Glycerol backbone
Two fatty acids attached instead of three
Third fatty acid replaced by phosphate group



The fatty acids are nonpolar and hydrophobic
The phosphate group is polar and hydrophilic
Molecules self arrange when placed in water



Polar phosphate “heads” next to water
Nonpolar fatty acid “tails” overlap and exclude water
Spontaneously form double layer & a sphere
33
Types of Lipids: Phospholipids

Phospholipids Form Membranes
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glycerol
O
Polar Head
–O
R O P O
1CH
2
O
2CH
O
CH2 CH2 CH2 CH CH
2
2 CH2 CH
2 CH2 CH
3
fatty acids
3CH
2
O
CH2 CH2 CH
CH =
2 CH2 CH2 CH2 CH2
O
Nonpolar Tails
outside cell
inside cell
phosphate
a. Phospholipid structure
b. Plasma membrane of a cell
34
Types of Lipids: Steroids & Waxes


Steroids

Cholesterol, testosterone, estrogen

Skeletons of four fused carbon rings
Waxes

Long-chain fatty acid bonded to a long-chain
alcohol

High melting point

Waterproof

Resistant to degradation
35
Steroid Diversity
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OH
CH3
CH3
O
b. Testosterone
CH3
HC
CH3
(CH2)3
HC
OH
CH3
CH3
CH3
CH3
HO
c. Estrogen
HO
a. Cholesterol
© Ernest A. Janes/Bruce Coleman, Inc.
36
Waxes
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
a.
b.
a: © Das Fotoarchiv/Peter Arnold, Inc.; b: © Martha Cooper/Peter Arnold, Inc.
37
Proteins

Functions


Support proteins

Keratin - makes up hair and nails

Collagen - support many of the body’s structures e.g. tendons, skin
Enzymes – Almost all enzymes are proteins

Acts as organic catalysts to accelerate chemical reactions within cells

Transport – Hemoglobin; membrane proteins

Defense – Antibodies

Hormones are regulatory proteins that influence the metabolism of
cells e.g. insulin

Motion – Muscle proteins, microtubules
38
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Protein Subunits: The Amino Acids

Proteins are polymers of amino acids
 Each amino acid has a central carbon atom (the
alpha carbon) to which are attached




a hydrogen atom,
an amino group –NH2,
A carboxylic acid group –COOH,
and one of 20 different types of –R (remainder) groups

There are 20 different amino acids that make up
proteins
 Amino acids differ according to their particular
R group
40
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Structural Formulas for the 20 Amino Acids
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Sample Amino Acids with Nonpolar (Hydrophobic) R Groups
H
H
H3N+
O
C
H3N+
C
(CH2)2
O–
H
O
C
C
CH
H3C
H3N+
O
H
O
H3N+
C
C
O–
CH2
CH
methionine (Met)
phenylalanine (Phe)
H
H2N+
C
H2C
CH2
CH3 CH3
CH3
valine (Val)
H
O–
CH2
S
CH3
H
C
C
C
O–
CH2
leucine (Leu)
proline (Pro)
Sample Amino Acids with Polar (Hydrophilic) R Groups
H
H3N+
H
O
H3N+
C
C
O–
CH2
C
H
O
H3N+
C
O–
CH2
H
O
C
H3N+
C
O–
CH2
H3N+
NH2
O
C
C
CH2
H
O
O–
H3N+
O–
CH
OH
O
asparagine (Asn)
O
glutamine (Gln)
OH
tyrosine (Tyr)
C
C
C
NH2
O–
C
serine (Ser)
H
C
(CH2)2
OH
SH
cysteine (Cys)
O
C
CH3
threonine (Thr)
Sample Amino Acids with Ionized R Groups
H
H
H3N+
C
O
H3N+
C
CH2
C
O–
H
O
C
H
O–
H3N+
O
C
CH2
CH2
CH2
C
COO–
N+H3
CH2
glutamic acid (Glu)
lysine (Lys)
–O
C
O
O–
O
O–
H3N+
O
C
C
CH2
NH
C
aspartic acid (Asp)
H
C
(CH2)3
C
CH2
H3N+
N+H2
NH2
arginine (Arg)
O–
NH
N+H
histidine (His)
42
Proteins: The Polypeptide Backbone

A peptide bond is a covalent bond between two
amino acids (AA)

COOH of one AA covalently bonds to the NH2 of the
next AA

Two AAs bonded together – Dipeptide

Three AAs bonded together – Tripeptide

Many AAs bonded together – Polypeptide

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
43
Synthesis and Degradation of a Peptide
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
amino group
peptide bond
acidic group
dehydration reaction
hydrolysis reaction
amino acid
amino acid
dipeptide
water
Protein: Levels of Structure


Protein shape (3-D structure) determines the function of
the protein in the organism
Proteins can have up to four levels of structure

Primary:



Secondary:



The way the amino acid chain coils or folds
Describing the way a knot is tied
Tertiary:



Literally, the sequence of amino acids
A string of beads (up to 20 different colors)
Overall three-dimensional shape of a polypeptide
Describing what a knot looks like from the outside
Quaternary:


Consists of more than one polypeptide
Like several completed knots glued together
45
Levels of Protein Organization
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
H3N+
Primary Structure
amino acid
This level of structure
is determined by the
sequence of amino
acids that join to form
a polypeptide.
peptide bond
COO–
hydrogen bond
hydrogen bond
Secondary Structure
Hydrogen bonding
between amino acids
causes the polypeptide
to form an alpha helix
or a pleated sheet.
(alpha) helix
(beta) sheet = pleated sheet
Tertiary Structure
Due in part to covalent
bonding between R
groups the polypeptide
folds and twists giving
it a characteristic
globular shape.
disulfide bond
Quaternary Structure
This level of structure
occurs when two or more
polypeptides join to form
a single protein.
46
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47
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
48
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Protein-folding Diseases

Assembly of AA’s into protein extremely complex

Process overseen by “chaperone” molecules

Inhibit incorrect interactions between R groups as
polypeptide grows

Defects in these chaperones can corrupt the tertiary
structure of proteins

Mad cow disease could be due to mis-folded proteins
50
Nucleic Acids
Polymers of nucleotides
 Very specific cell functions


DNA (deoxyribonucleic acid)
Double-stranded helical spiral (twisted ladder)
 Serves as genetic information center
 In chromosomes


RNA (ribonucleic acid)
Part single-stranded, part double-stranded
 Serves primarily in assembly of proteins
 In nucleus and cytoplasm of cell

51
The Nucleotides of Nucleic Acids

Three components:

A phosphate group,

A pentose sugar (ribose or deoxyribose), and

A nitrogenous base (4 kinds in DNA, 3 kinds in RNA, 3
common to both

Nucleotide subunits connected end-to-end to make
nucleic acid

Sugar of one connected to the phosphate of the next

Sugar-phosphate backbone
52
Nucleotides
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nitrogencontaining
base
phosphate
pentose sugar
a. Nucleotide structure
deoxyribose (in DNA)
ribose (in RNA)
b. Deoxyribose versus ribose
Purines
Pyrimidines
cytosine
thymine in DNA
c. Pyrimidines versus purines
uracil in RNA
adenine
guanine
53
DNA Structure
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
A
G
T
T
C
C
A
G
C Cytosine
S Sugar
G Guanine
A Adenine
P Phosphate T Thymine
a. Space-filling model
b. Double helix
© Photodisk Red/Getty Images
54
RNA Structure
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P
S
Nitrogen-containing bases
P
S
Backbone
P
C Cytosine
S Ribose
G Guanine
A Adenine
S
P Phosphate U Uracil
P
S
55
Complementary Base Pairing
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sugar
N
guanine (G)
sugar
cytosine (C)
sugar
sugar
adenine (A)
thymine (T)
c. Complementary base pairing
56
Comparison of DNA & RNA
57
Other Nucleic Acids

ATP (adenosine triphosphate) is composed of
adenine, ribose, and three phosphates

In cells, one phosphate bond is hydrolyzed –
Yields:


The molecule ADP (adenosine diphosphate)

An inorganic phosphate molecule pi

Energy
Other energy sources used to put ADP and pi
back together again
58
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ATP
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a.
adenosine
triphosphate
c.
H2O
P
adenosine
b.
P
P
triphosphate
ATP
P
adenosine
P
diphosphate
+
P
+
energy
phosphate
ADP
c: © Jennifer Loomis/Animals Animals/Earth Scenes
60
Review

Organic vs Inorganic

Functional Groups and Isomers

Macromolecules

Carbohydrates

Lipids

Proteins

Nucleic Acids
61
Chapter 3: pp. 37-58
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10th Edition
Sylvia S. Mader
The Chemistry of
Organic Molecules
BIOLOGY
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PowerPoint® Lecture Slides are prepared by Dr. Isaac Barjis, Biology Instructor
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62