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The Chemical Building
Blocks of Life: The Macromolecules
1

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Big Ideas
Introduction to Organic
Compounds
Carbohydrates
Lipids Proteins Nucleic Acids

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Carbon: The Framework of Biological Molecules
• Life’s molecular diversity is based on the properties of carbon
• Almost all the molecules a cell makes are composed of carbon
bonded to...
• other carbons
• atoms of other elements (O, N, S, P, H)
• Carbon-based molecules are called organic molecules

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be scanned, copied or duplicated, or posted to a publicly accessible website, in whole or in part.
The Chemistry of Biology – Basis of Macromolecules
• The molecules of life—carbohydrates, proteins,
lipids, and nucleic acids—are organic molecules.
• Organic
− Type of molecule that consists primarily of carbon
and hydrogen atoms
• Carbon atoms bond covalently with up to four
other atoms, often forming long chains or rings.

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Carbon: Framework of Biological Molecules
• Methane and other compounds
composed of only carbon and
hydrogen are called hydrocarbons.
• Nonpolar
• Functional groups add
chemical properties
• A carbon skeleton is a chain of
carbon atoms that can differ in
length and be
• Straight
• Branched
• Arranged in rings
• Form balls, tubes, or coils

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Carbon: The Framework of Biological Molecules
Butane
Length: Carbon skeletons vary
in length.
Propane 1-Butene 2-Butene
Double bonds: Carbon skeletons may have
double bonds, which can vary in location.
Double bond
Isobutane Cyclohexane Benzene
Branching: Carbon skeletons may
be unbranched or branched.
Rings: Carbon skeletons may be arranged in
rings. (In the abbreviated ring structures, each
corner represents a carbon and its attached
hydrogens.)
Ethane

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Properties of Structure
• Compounds with the same
molecular formula but different
structural arrangements are called
isomers
• Structural isomers
• Cis-trans isomers (or
stereoisomers)
• Enantiomers
• Chiral compounds
• D-sugars & L-amino acids
(a) Structural isomers
(b) Cis-trans isomers
(c) Enantiomers
cis isomer: The two Xs
are on the same side.
trans isomer: The two Xs
are on opposite sides.
CO2 HCO2 H
CH 3
H NH 2
L isomer
NH 2
CH 3
H
D isomer

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Carbon: The Framework of Biological Molecules
• The unique properties of an organic compound depend on
• the size and shape of its carbon skeleton
• the groups of atoms that are attached to that skeleton
• The sex hormones testosterone and estradiol (a type of
estrogen) differ only in the groups of atoms attached to the
skeleton structure

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Carbon: The Framework of Biological Molecules
• There are four classes of molecules important to organisms:
1. Carbohydrates
2. Lipids
3. Proteins
4. Nucleic acids

10
Macromolecules
• Polymer – built by linking monomers
• Monomer – small, similar chemical subunits

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be scanned, copied or duplicated, or posted to a publicly accessible website, in whole or in part.
From Structure to Function
• Cells assemble large polymers from smaller monomers and break apart polymers
into component monomers.
• The four classes of biological molecules contain very large molecules
• Often called Macromolecules because of their large size
• Monomers
• Molecules that are subunits of polymers
• Examples: Simple sugars, fatty acids, amino acids, and nucleotides
• Polymers
− Molecules that consist of multiple monomers
− Examples: Carbohydrates, lipids, proteins, and nucleic acids

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Carbon: The Framework of Biological Molecules
• Monomers linked together to form polymers through Condensation
(dehydration synthesis) Reactions, which remove water
• Polymers are broken apart by Hydrolysis, the addition of water
• These reactions are mediated by enzymes, specialized
macromolecules that catalyze (speed up) chemical reactions in cells

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be scanned, copied or duplicated, or posted to a publicly accessible website, in whole or in part.
Enzyme-Driven Reactions
• Enzyme-driven reactions construct large molecules from smaller
subunits and break large molecules into smaller ones.
• Enzyme
− Molecule that speeds up a reaction without being changed by
it = Catalyst
• Metabolism
− All enzyme-mediated reactions within cells to acquire and use
energy to stay alive, grow, and reproduce

15
Carbohydrates
• Molecules with a 1:2:1 ratio of carbon,
hydrogen, oxygen
• Empirical formula (CH 2 O)n
• C—H covalent bonds hold much energy
• Recall: Potential Energy – Bond Energy
– Carbohydrates are good energy storage molecules
– Examples: sugars, starch, glucose

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Carbohydrates: Energy Storage and Structural Molecules
• Monosaccharides are
• the main fuels for cellular work
• used as raw materials to manufacture other organic molecules
• Monosaccharides are classified by
• the location of the carbonyl group
• the number of carbons in the carbon skeleton

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Carbohydrates: Energy Storage and Structural Molecules
• Often shown in linear form, with numbered carbons
• But in aqueous environment, many form rings

18
Carbohydrates: Monosaccharides
• Simplest carbohydrate
• 6 carbon sugars play important roles
• Glucose: C 6H 12O6
• 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

19
Carbohydrates: Disaccharides
• 2 monosaccharides linked together by Dehydration Synthesis
• Used for sugar transport or energy storage
• Examples:
• Sucrose (glucose + fructose)
• Maltose (glucose + glucose)
• Lactose (glucose + galactose)
OH
SucroseFructoseα-glucose
HO
CH 2OH
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
H 2O
CH 2OH CH 2OH CH 2OH CH 2OH CH 2OH
CH 2OH CH 2OH
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20
Carbohydrates: Polysaccharides
• Long chains of monosaccharides
– Linked through dehydration
synthesis
• Energy storage
– Plants make and use starch
– Animals make and use
glycogen
• Structural support
– Plants use cellulose
– Arthropods and fungi use chitin

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Carbohydrates: Energy Storage and Structural Molecules
(a) a and b glucose
ring structures
(b) Starch: 1–4 linkage of a glucose monomers (c) Cellulose: 1–4 linkage of b glucose monomers
a Glucose b Glucose
4 1 4 1
41 41

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be scanned, copied or duplicated, or posted to a publicly accessible website, in whole or in part.
Some Complex Carbohydrates

Lipids

24
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
• Important in long-term energy storage
• Contain twice as much energy as a polysaccharide (g for g)
• Consist mainly of carbon and hydrogen atoms linked by nonpolar
covalent bonds
• Most biologically important lipids are fats, phospholipids, and
steroids. Also include some vitamins

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Lipids: Hydrophobic Molecules
• Lipids differ from carbohydrates, proteins, and
nucleic acids in that they are
• not huge molecules
• not built from monomers
• Lipids vary a great deal in structure and function
• Three main types of lipids:
• Fats
• Phospholipids
• Steroids

Fats
• A fat is a large lipid made from two smaller
molecules:
• glycerol
• fatty acids
• Triglycerides
– Composed of 1 glycerol and 3 fatty acids
• The most abundant source of energy in
vertebrates
− Stored in adipose tissue that insulates the
body
− Lipid with one, two, or three fatty acid tails

Starr, Biology Today and Tomorrow with Physiology, 6th Edition. © 2021 Cengage. All Rights Reserved. May not
be scanned, copied or duplicated, or posted to a publicly accessible website, in whole or in part.
Fatty acids
Chain length varies
– Even number of Carbons
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
• Hydrogenated vegetable oils are
unsaturated fats that have been
converted to saturated fats by
adding hydrogen
• Associated with health risks

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Lipids: Hydrophobic Molecules
• A fatty acid can link to glycerol by
a dehydration reaction, forming an
ester bond, and releasing a water
molecule
• Fats are often called Triglycerides
because of their structure
• 1 glycerol + 3 fatty acids
• Fatty acids do not to be identical
• Chain length varies

Lipids - Triglycerides
Saturated Fat Unsaturated Fat

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Phospholipids: Hydrophobic Molecules
• Phospholipids are the major component of all biological membranes
• Phospholipids are
composed of:
• Glycerol
• Two fatty acids
(nonpolar “tails”)
• Phosphate
group (polar
“head)

31
• 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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• Phospholipid bilayer – more complicated
structure where 2 layers form
– Hydrophilic heads point outward
– Hydrophobic tails point inward toward each
other
32
b.
Water
Water
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Starr, Biology Today and Tomorrow with Physiology, 6th Edition. © 2021 Cengage. All Rights Reserved. May not
be scanned, copied or duplicated, or posted to a publicly accessible website, in whole or in part.
Phospholipids – Basis of Membrane Structure

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be scanned, copied or duplicated, or posted to a publicly accessible website, in whole or in part.
Waxes and Steroids
• Wax
− Water-repellent lipid with long fatty-acid
tails bonded to long-chain alcohols or
carbon rings
• Steroid
− A type of lipid with four carbon rings and
no fatty acid tails
− Steroids have two principal biological
functions: as important components of
cell membranes that alter membrane
fluidity; and as signaling molecules

Proteins

Tab. 3.2

Starr, Biology Today and Tomorrow with Physiology, 6th Edition. © 2021 Cengage. All Rights Reserved. May not
be scanned, copied or duplicated, or posted to a publicly accessible website, in whole or in part.
Proteins
• Protein - Polymer
− Organic compound that consists of one or more chains of
amino acids (polypeptides)
− Function is determined by its structure.
• Amino acid - Monomer
− Small organic compound with a carboxyl group, amine
group, and a characteristic side group (R)

38
CH 2
CH 2
CH 3
CH 2
OH H O
S H
S
CH 2
CH 2
O
CH 2
NH 2+
C C O–H 3 N +
C C O–H 3 N +
C C O–H 3 N +
C C O–
H 3 N +
C C O–
H 3 N +
C C O–
H 3 N +
C C O–H 3 N +
C C O–H 3 N +
C C O–
H 3 N +
C C O–H 3 N +
C C O–H 3 N +
C C O–
H 3 N +
C C O–
H 3 N +
C C O–H 3 N +
C C O–H 3 N + C C O–H 3 N + C C O–
H 3 N +
C C O–
H 3 N +
CH C O– C C O–
NH 3+
CH 3
OH
CH 2
OH
OH
H
OH
OH
CH 3CH 3
CH
CH 2
OH
CH 3CH 3
CH
CH 2
OH
NH 2O
C
CH 2
OH
O –
O
C
CH 2
CH 2
CH 2 NH 3+
OH
CH 2
CH 2
CH 2
OH
O–O
C
CH 2
CH 2
OH
NH 2O
C
H C CH 3
CH 2
CH 3
OH
H C OH
CH 3
OH
CH 2
CH
C N
HC NH +
H O
H
CH 2
NH
C
H O
CH 2
H O
OH
CH 2
H O
CH 2
CH 2
NH
NH 2
C
OH
CH 2
NH 3+
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
NonaromaticAromaticSpecial function
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Valine
(Val)
Amino Acids

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be scanned, copied or duplicated, or posted to a publicly accessible website, in whole or in part.
Peptide Bonds
• Amino acids are linked into chains by peptide bonds.
− A bond between the amine group of one amino acid and the
carboxyl group of another
• Polypeptide
− Chain of amino acids linked by peptide bonds

40
• Amino acids joined by Dehydration Synthesis
– Peptide Bond
RH
H
R
H O
R
OH
RH
OH
H 2 O
H
O
H
OH OH
OHH
CC C C
CC CC
N
N N
NH H
Amino acid
Dipeptide
Amino acid

41
4 Levels of Protein 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
a helix
b sheet

4 Levels of Protein 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
42

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be scanned, copied or duplicated, or posted to a publicly accessible website, in whole or in part.
How Protein Structures Arises

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
44

45
Domain 3 Domain 2
Domain 1
DomainsMotifs
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β-α-β
motif
Helix-turn-Helix
motif

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be scanned, copied or duplicated, or posted to a publicly accessible website, in whole or in part.
The Importance of Protein Structure
• Changes in a protein’s structure may also alter its function.
• Denature
− To unravel the shape of a protein or other large biological molecule
• Prion
− A misfolded protein that becomes infectious
− Example: Mad cow disease (BSE) in cattle
− Example: vCJD in humans

Denaturation
• Protein loses
structure and function
• Due to environmental
conditions
– pH
– Temperature
– Ionic concentration of
solution
47
Properly folded protein
Denaturation
Denatured
protein
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Proteins: Molecules with Diverse Structures and Functions
• Chaperone proteins
• Help protein fold correctly
• Deficiencies in chaperone proteins implicated in certain diseases
• Cystic fibrosis (hereditary disorder) – in some individuals, protein
appears to have correct amino acid sequence but fails to fold

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be scanned, copied or duplicated, or posted to a publicly accessible website, in whole or in part.
Nucleic Acids
• Nucleotide
− Monomer of nucleic acids
− Has a five-carbon sugar, a nitrogen-containing base, and
phosphate groups
• Nucleic acids
− Polymers of nucleotide monomers joined by sugar–phosphate
bonds
− Function as energy carriers, enzyme helpers, chemical
messengers, and subunits of DNA and RNA

51
5 ́
2
8
7 6
39
4
5
1
NH 2
O
P
O-
– O O CH 2
Phosphate group
Sugar
Nitrogenous base
OH
NN
N
O
4 ́ 1 ́
2 ́3 ́
H in DNA
OH in RNA
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Nucleotide

52
5′
3′
P
P
P
P
OH
Phosphate group
O
O
NH 2CC
NN
N
C
H
N
C
CH
O
H
H
OC
NC
H
N
C
NH 2
H
CH
a.
b.
O
O
O
C
NC
H
N
C
H 3C
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
NH 2
GuanineAdenine
PurinesPyrimidines
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Cytosine
(both DNA and RNA)
Thymine
(DNA only)
Uracil
(RNA only)

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be scanned, copied or duplicated, or posted to a publicly accessible website, in whole or in part.
Nucleic Acid Structure

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 54

55
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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

56
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

57
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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

58
Other Nucleotides
• ATP: adenosine triphosphate
– Primary energy currency of the cell
• NAD + and FAD +
– Electron carriers for many cellular reactions