Chapter 3: pp. 37-58
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10th Edition
Sylvia S. Mader
The Chemistry of
Organic Molecules
BIOLOGY
© The McGraw Hill Companies, Inc./John Thoeming, photographer
PowerPoint® Lecture Slides are prepared by Dr. Isaac Barjis, Biology Instructor
Copyright © The McGraw Hill Companies Inc. Permission required for reproduction or display
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
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
5
Octane & Cyclohexane
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octane
cyclohexane
6
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
7
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
8
Hexose Isomers
9
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
10
Common Foods
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11
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
12
Dehydration
Short polymer
Unlinked monomer
Dehydration
reaction
Longer polymer
Hydrolysis
Hydrolysis
Dehydration and Hydrolysis
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
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
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 (unbranched) and amylopectin (branched) 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
Complex Carbohydrates
24
Starch Structure and Function
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starch
granule
a. Starch
250mm
© Jeremy Burgess/SPL/Photo Researchers, Inc.
25
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.
26
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
27
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.
28
Lipids

Lipids are varied in structure

Insoluble in water



Long chains of repeating CH2 units
Renders molecule nonpolar
Lack polar groups
29
Lipids

Fat provides insulation
and energy storage in
animals
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© Paul Nicklen/National Geographic/Getty
30
Types of Lipids
31
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
32
Types of Lipids: Triglycerides
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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
33
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
34
Animal and Plant Fats
Most plant fats are unsaturated and most
animal fats are saturated.
 Butter and lard are solids at room
temperature.
 Too much saturated and trans fats can lead
to atherosclerosis. Lipids containing
deposits called plaques build up within the
walls of blood vessels, reducing blood flow.

Atherosclerosis
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
37
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
38
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
39
CONNECTION
 Anabolic
•
steroids pose health risks
Anabolic steroids are natural and
synthetic variants of the male hormone
testosterone
– Build up bone and muscle mass
– Can cause serious health problems
Anabolic Steroids


Anabolic steroids are synthetic variants of
the male hormone testosterone – which
generally causes a build up in muscle mass
in males during puberty and maintains
masculine traits.
Positive uses of anabolic steroids

As a prescription drug, anabolic steroids are
used to treat general anemia and diseases that
destroy body muscle.
Negative effects of Anabolic
Steroids
•
•
•
•
•
Violent mood swings (“Roid Rage”)
Deep Depression
Alter cholesterol levels leading to high blood pressure and increasing
risk of cardiovascular problems.
Reduces the bodies natural output of male sex hormones – shrunken
testicles, reduced sex drive, infertility, and breast enlargement in men.
In women, use has been linked to menstrual cycle disruption and
development of masculine characteristics.
Waxes
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a.
b.
a: © Das Fotoarchiv/Peter Arnold, Inc.; b: © Martha Cooper/Peter Arnold, Inc.
43
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
44
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
45
Protein Structure
46
Structural Formulas for the 20 Amino Acids
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
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)
47
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
48
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
50
Levels of Protein Organization
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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.
51
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52
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
53
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
54
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

55
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
56
Nucleotides
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
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
57
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
58
RNA Structure
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
P
S
Nitrogen-containing bases
P
S
Backbone
P
C Cytosine
S Ribose
G Guanine
A Adenine
S
P Phosphate U Uracil
P
S
59
Complementary Base Pairing
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sugar
N
guanine (G)
sugar
cytosine (C)
sugar
sugar
adenine (A)
thymine (T)
c. Complementary base pairing
60
Comparison of DNA & RNA
61
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
62
ATP
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
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
63
Review

Organic vs Inorganic

Functional Groups and Isomers

Macromolecules

Carbohydrates

Lipids

Proteins

Nucleic Acids
64
Chapter 3: pp. 37-58
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
10th Edition
Sylvia S. Mader
The Chemistry of
Organic Molecules
BIOLOGY
© The McGraw Hill Companies, Inc./John Thoeming, photographer
PowerPoint® Lecture Slides are prepared by Dr. Isaac Barjis, Biology Instructor
Copyright © The McGraw Hill Companies Inc. Permission required for reproduction or display
65