BIOLOGY

Chapter 3: pp. 37-58

10th Edition

The Chemistry of

Sylvia S. Mader
Organic Molecules
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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
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consist of b. Shell contains chitin.

cellulose
 Cell wall of fungi
and shell of crab
contain chitin
 Bacterial cell wall
contain
peptidoglycan 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

 Oftenbonds 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 Structure Compound Significance

Hydroxyl R OH Alcohol Polar, forms

as in hydrogen bond
ethanol
Present in sugars,
some amino acids

Carbonyl O Aldehyde Polar

R C as in
H Present in sugars
formaldehyde

O Ketone Polar
as in
R C R acetone Present in sugars

Carboxyl O Carboxylic acid Polar, acidic

(acidic) R C as in
OH acetic acid Present in fatty
acids, amino acids

Amino H Amine Polar, basic, forms

R N as in tryptophan hydrogen bonds
H
Present in amino acids

Sulfhydryl R SH Thiol Forms disulfide bonds

as in ethanethiol
Present in some
amino acids

Phosphate O Organic Polar, acidic

phosphate
R O P OH as in Present in
OH phosphorylated nucleotides,
molecules 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 dihydroxyacetone

H H O H O H

H C C C H H C C C H

OH OH OH 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:

11
Common Foods
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12
Animation

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Dehydration and Hydrolysis
 Dehydration - Removal of water molecule
 Used to connect monomers together to make polymers
 Polymerization of glucose monomers to make starch

 Hydrolysis - Addition of water molecule

 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 monomer

dehydration H2O
reaction

monomer monomer

a. Synthesis of a biomolecule

monomer OH H monomer

hydrolysis
reaction H2O

monomer 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 CH2OH
H C O H H O H
H C
C
OH H OH H
HO C C OH HO OH
a. b.
H OH H OH
C6H12 O6
O O

c. d.
© Steve Bloom/Taxi/Getty

18
Synthesis and Degradation
of Maltose, a Disaccharide
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CH2OH CH2OH CH2OH CH2OH

O H H O O O
dehydration reaction
O H2O
OH hydrolysis reaction
HO

glucose C6H12 O6 glucose C6H12 O6 maltose C12 H22 O11 water

monosaccharide + monosaccharide disaccharide + water

Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

CH2OH CH2OH
O O

glucose O fructose
sucrose 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
C H O5 & C5H10O4
5 10

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 250µ m
© Jeremy Burgess/SPL/Photo Researchers, Inc.

24
Glycogen Structure and Function
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glycogen
granule

b . Glycogen 150 nm
© Don W. Fawcett/Photo Researchers, Inc.

25
Cellulose Structure and Function
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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 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

and energy storage in

animals

© 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 H H H H O H H H H
O
C C C C C H H C O C C C C C H
H C OH HO
H H H H H H H H

H H H H H H dehydration reaction O H H H H H H
O
+ C C C C C C C H H C O C C C C C C C H
+3 H O
2
H C OH HO hydrolysis reaction
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
H C OH HO C C
H C H H C
H H H H
H H
kink kink H

glycerol 3 fatty acids fat molecule 3 water

a. Formation of a fat molecules

30
Types of Lipids: Triglycerides
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corn corn oil

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 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
O
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 H H H

saturated fatty acid with no double bonds saturated fat

b.ypes
T of fatty acids c. T
ypes 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 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH
CH2 CH2 CH2 2 CH2 CH2 CH
C CH2 3
1
CH2 O
Polar Head
fatty acids
–
O 2
CH O O

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

outside cell
inside cell

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
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
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, 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
Animation

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Protein Subunits: The Amino Acids
 Proteinsare 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 –NH ,
2
 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
Animation

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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 H H
O O

H H3N+ C C H3N+ C C H3N+ C C H

O H
O O– CH2 O–
H3N+
C C (CH2)2 CH2 H2N +
C C

O– CH H2C O–
CH S CH2
H3C CH3 CH3 CH3 CH2
CH3
valine (Val) methionine (Met) phenylalanine (Phe) leucine (Leu) proline (Pro)

Sample Amino Acids with Polar (Hydrophilic) R Groups

H H H H
O O O O
H3N+ C C H3N+ C C H3N+ C C H3N+ C C
O– O–
CH2 O– CH2 O– CH2 (CH2)2

SH OH C
cysteine (Cys) H serine (Ser)
O NH2 O

H3N+ C C H OH glutamine (Gln)

O
O– tyrosine (Tyr)
CH2 H3N+ C C

C CH O–

NH2 O OH CH3
asparagine (Asn) threonine (Thr)

Sample Amino Acids with Ionized R Groups

H H O
O
H3N+ H3N +
C C H O
H C C H
O O
O– (CH2)3 O– H3N+ C C
H3N+ C C CH2 H3N+ C C
O– NH CH2 O–
CH2 CH2 CH2 O–
NH
CH2 CH2 C C N+H2

COO– O
–
O NH2 N+H
N+H3
aspartic acid (Asp) arginine (Arg) histidine (His)
glutamic acid (Glu) lysine (Lys)

42
Proteins: The Polypeptide Backbone
Apeptide 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

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amino group acidic group peptide bond

dehydration reaction

hydrolysis reaction

amino acid amino acid water

dipeptide
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:
 Literally, the sequence of amino acids
 A string of beads (up to 20 different colors)
 Secondary:
 The way the amino acid chain coils or folds
 Describing the way a knot is tied
 Tertiary:
 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
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H3N +

Primary Structure

This level of structure amino acid

peptide bond
is determined by the COO–
sequence of amino
acids that join to form
a polypeptide.

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
Animation

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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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nitrogen-
phosphate containing
base

pentose sugar deoxyribose (in DNA) ribose (in RNA)

a. Nucleotide structure b. Deoxyribose versus ribose

Pyrimidines Purines

cytosine thymine in DNA uracil in RNA adenine guanine

c. Pyrimidines versus purines

53
DNA Structure
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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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S Nitrogen-containing bases

Backbone

P
C Cytosine S Ribose
G Guanine A Adenine S
P Phosphate U Uracil

55
Complementary Base Pairing

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sugar
N
sugar

guanine (G) 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
 Incells, 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
Animation

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ATP
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a. adenosine triphosphate c.

H2O

P P P P P + P + energy

adenosine triphosphate adenosine diphosphate phosphate

b. ATP ADP

c: © Jennifer Loomis/Animals Animals/Earth Scenes

60
Review
 Organic vs Inorganic
 Functional Groups and Isomers
 Macromolecules

 Carbohydrates

 Lipids

 Proteins

 Nucleic Acids
61
 BIOLOGY
Chapter 3: pp. 37-58
10th Edition

The Chemistry of

Sylvia S. Mader
Organic Molecules
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

© The McGraw Hill Companies, Inc./John Thoeming, photographer

PowerPoint® Lecture Slides are prepared by Dr. Isaac Barjis, Biology Instructor 62
Copyright © The McGraw Hill Companies Inc. Permission required for reproduction or display