Carbon is the main element that makes up biological molecules. It can form up to four covalent bonds and its ability to do so allows it to form complex structures like carbohydrates, lipids, proteins, and nucleic acids. These macromolecules are made through the linking of smaller monomer units like monosaccharides, amino acids, and nucleotides. The three main classes of macromolecules are carbohydrates, which serve structural and energy roles; proteins, which have many functions including enzyme catalysis; and nucleic acids like DNA and RNA, which encode genetic information and direct protein synthesis.

1. Chapter 03
Lecture and
Animation Outline
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1

2. The Chemical Building
Blocks of Life
Chapter 3
2

3. 3
Carbon
• Framework of biological molecules
consists primarily of carbon bonded to
– Carbon
– O, N, S, P or H
• Can form up to 4 covalent bonds
• Hydrocarbons – molecule consisting only
of carbon and hydrogen
– Nonpolar
– Functional groups add chemical properties

4. 4
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Hydroxyl
Carbonyl
Carboxyl
Amino
Sulfhydryl
Phosphate
Methyl
Example
OH
O
C
O
OH
C
H
H
N
S H
O
proteins
proteins
H
H
Glycerol phosphate
Alanine
Cysteine
Alanine
Acetic acid
Acetaldehyde
Ethanol
COOH
NH2
HH
H
HH
C OHC
O
H C C
H
H
H
H C
O
OHH
C
O H
N
H
H
CH3
H C HSCH2
NH2
OH OH H
P
O
P O–
O–
O
OCCCH
H H H
O H
HO C C
H C H
H
O–
O–
H
C
HO C C
H
Found
In
carbo-
hydrates,
proteins,
nucleic
acids,
lipids
carbo-
hydrates,
nucleic
acids
proteins,
lipids
proteins,
nucleic
acids
nucleic
acids
Functional
Group
Structural
Formula

5. 5
Isomers
• Molecules with the same molecular or
empirical formula
– Structural isomers
– Stereoisomers – differ in how groups attached
• Enantiomers
– mirror image molecules
– chiral
– D-sugars and L-amino acids

6. 6
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C
W
Y
W
Y
C
Z
X
Z
X
Mirror

7. 7
Macromolecules
• Polymer – built by linking monomers
• Monomer – small, similar chemical subunits

8. 8
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
O
P
P
OH
HO
H
OH
H
OH
OH
H
H
H
O
Cellular Structure Polymer Monomer
Chromosome DNA strand Nucleotide
MonosaccharideStarchStarch grains in a chloroplast
5-carbon sugar
Phosphate
group
Nitrogenous base
CH2OH
CarbohydrateNucleicAcid
P
P
P
P
P
P
P
G
C
T
A
A
T
P
A
P
P
P
P
G
C
P
P
T
A
G
C
P

9. 9
Ala
Ala
Val
Val
Ser O
N
H
C
H
OH
H
C
CH3
Intermediate filament Polypeptide Amino acid
Protein
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
HO H H H H H H H H H H
HHO C C C C C C C C C C C C
H H H H H H H H H H H
Adipose cell with fat droplets
Triglyceride
Fatty acid
Lipid

10. 10
• Dehydration synthesis
– Formation of large molecules by the removal of water
– Monomers are joined to form polymers
• Hydrolysis
– Breakdown of large molecules by the addition of
water
– Polymers are broken down to monomers
HO
HO H
HO HH HHO
HO H HHO
a. Dehydration reaction b. Hydrolysis reaction
H2O H2O
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

11. 11
Carbohydrates
• Molecules with a 1:2:1 ratio of carbon,
hydrogen, oxygen
• Empirical formula (CH2O)n
• C—H covalent bonds hold much energy
– Carbohydrates are good energy storage
molecules
– Examples: sugars, starch, glucose

12. 12
Monosaccharides
• Simplest carbohydrate
• 6 carbon sugars play important roles
• Glucose C6H12O6
• Fructose is a structural isomer of glucose
• Galactose is a stereoisomer of glucose
• Enzymes that act on different sugars can
distinguish structural and stereoisomers of
this basic six-carbon skeleton

13. 13
H
CH2OH
H
OH
OH H
H
H
C
CC
C
C
C
C
H
C H
HO
OHH
OHH C
OHH C
OHH C
H
OH
C HH
OH
H
OH
H
OH
H
OH
H
OH H
H
H
C
CC
C
C O
OH
OH H
H
H
C
CC
C
OC
OH
OH
O
H
23
5
14
6
5
4
3
2
1
23
5
6
14
23
5
14
α-glucose
or
β-glucose
O
O
CH2OH
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14. 14
Fructose Glucose Galactose
H OH
O
C
C
C
C
C
C
H
H
HO H
H OH
H OH
H OH
H
OC
C
C
C
C
H
H
HO H
OH
H OH
H OH
OC
C
C
C
C
C
H
H
H
HO H
OH
H OH
H OH
CH OH HO H
Stereo-
isomer
Structural
isomer
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15. 15
Disaccharides
• 2 monosaccharides linked together by
dehydration synthesis
• Used for sugar transport or energy storage
• Examples: sucrose, lactose, maltose
OH
SucroseFructoseα-glucose
HO
CH2OH
H
OH
H
OH
H
H
H
O
H
OH H
H
O
HO
H
OH
H
OH OH
H
H
O
H OH
OH H
HO
+
a. b.
Maltose
HO
H
OH
H
OH OH
H
H
O H
OH
H
OH
OH
H
H
H
O
OH
HO
H2O
CH2OH CH2OH CH2OH CH2OH CH2OH
CH2OH CH2OH
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16. 16
Polysaccharides
• Long chains of monosaccharides
– Linked through dehydration synthesis
• Energy storage
– Plants use starch
– Animals use glycogen
• Structural support
– Plants use cellulose
– Arthropods and fungi use chitin

17. 17
Glycogen
Amylose + Amylopectin
b.
a. c. 3.3 µm
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α-glucose
HO
CH2OH
H
OH
H
OH H
H
H
O
OH
4 1
α-1 4 linkages
CH2OH
OH
H
OH H
H
O
CH2OH
OH
H
OH H
H
O
CH2OH
OH
H
OH H
H
O
O O
H
α-1 4 linkage
a-1
CH2OH
O
H
OH
H
OH H
H
H
O
CH2
H
OH
H
OH H
H
H
O
O
CH2OH
H
OH
H
OH H
H
H
O
6 linkage
b: © Asa Th oresen/Photo Researchers, Inc.; c: © J. Carson/Custom Medical Stock Photo
7.5 µm

18. 18
HO
CH2OH
H
OH
H
OH H
H
H
O
CH2OH
H H
OH
H
OH H
H
H
O
O
CH2OH
H
OH
H
OH H
H
H
O
OHH
H
OH H
H
CH2OH
O
β-1 4 linkages
OH
O O
O
4 1
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b: © Science VU/Visuals Unlimited
β-glucose
500 µmb.
a.

19. Nucleic acids
• Polymer – nucleic acids
• Monomers – nucleotides
– sugar + phosphate + nitrogenous base
– sugar is deoxyribose in DNA or ribose in RNA
– Nitrogenous bases include
• Purines: adenine and guanine
• Pyrimidines: thymine, cytosine, uracil
– Nucleotides connected by phosphodiester
bonds
19

20. 20
5 ́
2
8
7 6
39
4
5
1
NH2
O
P
O-
–
O O CH2
Phosphate group
Sugar
Nitrogenous base
OH
NN
N
O
4 ́ 1 ́
2 ́3 ́
H in DNA
OH in RNA
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21. 21
5′
3′
P
P
P
P
OH
Phosphate group
O
O
NH2CC
NN
N
C
H
N
C
CH
O
H
H
OC
NC
H
N
C
NH2
H
CH
a.
b.
O
O
O
C
NC
H
N
C
H3C
CH
H
O
O
C
NC
H
N
C
H
CH
CC
NN
N
C
H
N
C
CH
H
O
4′
5′
1′
3′ 2′
4′
5′
1′
3′ 2′
4′
5′
1′
3′ 2′
4′
5′
1′
3′
2′
Phosphodiester bonds
5-carbon sugar
Nitrogenous
base
NH2
GuanineAdenine
PurinesPyrimidines
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Cytosine
(both DNA and RNA)
Thymine
(DNA only)
Uracil
(RNA only)

22. Deoxyribonucleic acid (DNA)
• Encodes information for amino acid
sequence of proteins
– Sequence of bases
• Double helix – 2 polynucleotide strands
connected by hydrogen bonds
– Base-pairing rules
• A with T (or U in RNA)
• C with G
22

23. 23
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5′ end
P
P
P
P
P
C
G
A
A
OH
T
T
Phosphodiester
bonds
3′ end
Sugar–phosphate
“backbone”
Hydrogenbonds
between
nitrogenous bases

24. 24
Ribonucleic acid (RNA)
• RNA similar to DNA except
– Contains ribose instead of deoxyribose
– Contains uracil instead of thymine
• Single polynucleotide strand
• RNA uses information in DNA to specify
sequence of amino acids in proteins

25. 25
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
P
P
P
P
P
P
P
P
P
P
P
P
P
P
P
G
C
G
C
T
A
A
A
A
T
T
G
Bases
Hydrogen bonding
Occurs between base-pairs
P
P
PP
P
P
P
G
G
C
A
A
U
U
Bases
Deoxyribose-
phosphate
backbone
Ribose-phosphate
backbone
RNA
DNA

26. 26
Other nucleotides
• ATP adenosine triphosphate
– Primary energy currency of the cell
• NAD+
and FAD+
– Electron carriers for many cellular reactions
4′
5
6
2
39
4
8
7
1′
3′ 2′
5′
1
CH2
OOO
O–
OH OH
NH2
N
N
N
N
O
–
O O O OP P P
Triphosphate group
5-carbon sugar
O
Nitrogenous base
(adenine)
O–
O–
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27. 27
Proteins
Protein functions include:
1. Enzyme catalysis
2. Defense
3. Transport
4. Support
5. Motion
6. Regulation
7. Storage

28. 28
• Proteins are polymers
– Composed of 1 or more long, unbranched
chains
– Each chain is a polypeptide
• Amino acids are monomers
• Amino acid structure
– Central carbon atom
– Amino group
– Carboxyl group
– Single hydrogen
– Variable R group

29. 29
CH2
CH2
CH3
CH2
OH H O
S H
S
CH2
CH2
O
CH2
NH2
+
C C O–
H3N+
C C O–
H3N+
C C O–
H3N+
C C O–
H3N+
C C O–
H3N+
C C O–
H3N+
C C O–
H3N+
C C O–
H3N+
C C O–
H3N+
C C O–
H3N+
C C O–
H3N+
C C O–
H3N+
C C O–
H3N+
C C O–
H3N+
C C O–
H3N+
C C O–
H3N+ C C O–
H3N+
C C O–
H3N+
CH C O–
C C O–
NH3
+
CH3
OH
CH2
OH
OH
H
OH
OH
CH3CH3
CH
CH2
OH
CH3CH3
CH
CH2
OH
NH2O
C
CH2
OH
O–
O
C
CH2
CH2
CH2 NH3
+
OH
CH2
CH2
CH2
OH
O–
O
C
CH2
CH2
OH
NH2O
C
H C CH3
CH2
CH3
OH
H C OH
CH3
OH
CH2
CH
C N
HC NH+
H O
H
CH2
NH
C
H O
CH2
H O
OH
CH2
H O
CH2
CH2
NH
NH2
C
OH
CH2
NH3
+
Nonpolar Polar uncharged Charged
Proline
(Pro)
Methionine
(Met)
Cysteine
(Cys)
Tryptophan
(Trp)
Tyrosine
(Tyr)
Phenylalanine
(Phe)
Glycine
(Gly)
Leucine
(Leu)
Glutamine
(Gln)
Isoleucine
(Ile)
Asparagine
(Asn)
Asparticacid
(Asp)
Histidine
(His)
Lysine
(Lys)
Glutamic acid
(Glu)
Threonine
(Thr) Arginine
(Arg)
(Ser)
Serine
(Ala)
Alanine
NonaromaticAromaticSpecialfunction
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Valine
(Val)

30. 30
• Amino acids joined by dehydration
synthesis
– Peptide bond
RH
H
R
H O
R
OH
RH
OH
H2O
H
O
H
OH OH
OHH
CC C C
CC CC
N
N N
NH H
Amino acid
Dipeptide
Amino acid

31. 31
4 Levels of structure
• The shape of a protein determines its
function
1. Primary structure – sequence of amino
acids
2. Secondary structure – interaction of groups
in the peptide backbone
α helix
β sheet

32. 4 Levels of structure
3. Tertiary structure – final folded shape of a
globular protein
– Stabilized by a number of forces
– Final level of structure for proteins consisting
of only a single polypeptide chain
4. Quaternary structure – arrangement of
individual chains (subunits) in a protein with
2 or more polypeptide chains
32

33. 33
•
•
•
•
•
•
•
•
•
•
••
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
••
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
Primary Structure
Secondary Structure Secondary Structure
Tertiary Structure Quaternary Structure
N
H
H H
C C C N C C NC
O
O H
OH H
R
R
R
β-pleated sheet α-helix
C
H
R
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
The primary structure can fold
Into a pleated sheet, or turn into a helix

34. Additional structural characteristics
• Motifs
– Common elements of secondary structure
seen in many polypeptides
– Useful in determining the function of unknown
proteins
• Domains
– Functional units within a larger structure
– Most proteins made of multiple domains that
perform different parts of the protein’s function
34

35. 35
Domain 3 Domain 2
Domain 1
DomainsMotifs
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
β-α-β
motif
Helix-turn-Helix
motif

36. 36
• Once thought newly made proteins folded
spontaneously
• Chaperone proteins help protein fold
correctly
• Deficiencies in chaperone proteins
implicated in certain diseases
– Cystic fibrosis is a hereditary disorder
• In some individuals, protein appears to have correct
amino acid sequence but fails to fold
Chaperones

37. 37
Chance for protein to refold
ADP + P
Cap
ATP
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Correctly
folded
protein
Misfolded
protein
Chaperone
protein

38. Denaturation
• Protein loses
structure and function
• Due to environmental
conditions
– pH
– Temperature
– Ionic concentration of
solution
38
Properly folded protein
Denaturation
Denatured
protein
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39. 39
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40. 40
Lipids
• Loosely defined group of molecules with
one main chemical characteristic
– They are insoluble in water
• High proportion of nonpolar C—H bonds
causes the molecule to be hydrophobic
• Fats, oils, waxes, and even some vitamins

41. 41
Fats
• Triglycerides
– Composed of 1 glycerol and 3 fatty acids
• Fatty acids
– Need not be identical
– Chain length varies
– Saturated – no double bonds between carbon
atoms
• Higher melting point, animal origin
– Unsaturated – 1 or more double bonds
• Low melting point, plant origin
– Trans fats produced industrially

42. 42
C
C
H
H
C
H
H
C
H
H
O
C
H
CH C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
C
H H
C
H
C C
HH H H
C
H
C C
H
O
H
HH H
C
H
H
C
H
H
O
C
H
CH C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
C
H
C
H
C
H
C
HH H
C
H
C
H
C
H H
O
H
H H
C
H
H
C
H
H
O
C
H
CH C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
C
H H
C
H H
C
H
C
H
H
C
H H
C
HH
C
H H
CO
O
C
H
C
H
H
C
H
H
C
H
H
CH C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
O
O
C
H
C
H
H
C
H
H
C
H
H
CH C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
O
O
C
H
C
H
H
C
H
H
C
H
H
CH C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
H
C
H
H
C
H
H
H
C
H
H
C
H
HO
H
H
Structural Formula Structural Formula
Space-Filling Model Space-Filling Model
a. b.
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43. 43
Phospholipids
• Composed of
– Glycerol
– 2 fatty acids – nonpolar “tails”
– A phosphate group – polar “head”
• Form all biological membranes

44. 44
NonpolarHydrophobicTailsPolarHydrophilicHeads
Choline
Phosphate
Glycerol
a. b. c. d.
CH2
CH2
CH2
H2C
O
O
O P
C
O O
OO
C
H
C
O-
N+
(CH3)3
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
F
a
t
t
y
a
c
i
d
F
a
t
t
y
a
c
i
d
CH
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH3
CH
CH2
CH2
CH2
CH2
CH2
CH2
CH
CH
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH3

45. 45
• Micelles – lipid molecules orient with polar
(hydrophilic) head toward water and
nonpolar (hydrophobic) tails away from
water
a.
Water
Lipid head
(hydrophilic)
Lipid tail
(hydrophobic)
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46. • Phospholipid bilayer – more complicated
structure where 2 layers form
– Hydrophilic heads point outward
– Hydrophobic tails point inward toward each
other
46
b.
Water
Water
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