Structure & Function of Macromolecules
Chapter 5
The Molecules of Life
Emergent properties – Complexity
increases at higher levels of the
organizational hierarchy of life
Small molecules combine to form huge
molecules – macromolecules
Macromolecules contain thousands of
covalently bonded atoms
Monomers and Polymers

Monomer – a molecule that can be bonded
to identical molecules to form chains

Polymer – a chain of monomers
◦ Carbohydrates
◦ Proteins
◦ Nucleic acids
The Synthesis and Breakdown of
Polymers

Dehydration reactions – monomers combine
to form polymers (produce water)
◦ Also called a condensation reaction

Hydrolysis reactions – polymers break down
into smaller units (consumes water)
LE 5-2
Short polymer
Unlinked monomer
Dehydration removes a water
molecule, forming a new bond
Longer polymer
Dehydration reaction in the synthesis of a polymer
Hydrolysis adds a water
molecule, breaking a bond
Hydrolysis of a polymer
Digestion is an example of hydrolysis
 Enzymes attack polymers & help break
them down
 The released monomers head for the blood
stream
 Then make their way to all cells for
reassembly into polymers

The Diversity of Polymers
 About
50 common monomers
 Variation
of polymers increases with
organizational hierarchy
 Can
consist of hundreds of monomers
Carbohydrates
 Monosaccharides-
simple sugars
(usually multiples of CH2O)
 Polysaccharides-
polymers made
of many simple sugars
Monosaccharides
◦ One carbonyl group
◦ Multiple hydroxyl group
◦ 3-7 carbons
◦ Examples: glucose, fructose,
galactose
LE 5-3
Triose sugars
(C3H6O3)
Pentose sugars
(C5H10O5)
Hexose sugars
(C5H12O6)
Glyceraldehyde
Ribose
Galactose
Glucose
Dihydroxyacetone
Ribulose
Fructose
 Monosaccharides-
cells
 Often
major fuel for
a linear skeleton
 Sometimes
form ring structures
◦ Aqueous solutions
LE 5-4
Linear and
ring forms
Abbreviated ring
structure
Disaccharides
Combination of 2 monosaccharides
 Joined by a glycosidic link
 Dehydration (condensation) reaction
 Examples

◦ Sucrose (table sugar) = glucose + fructose
◦ Lactose = glucose + galactose
◦ Maltose (malt sugar) = glucose + glucose
LE 5-5
Dehydration
reaction in the
synthesis of maltose
1–4
glycosidic
linkage
Glucose
Glucose
Dehydration
reaction in the
synthesis of sucrose
Maltose
1–2
glycosidic
linkage
Glucose
Fructose
Sucrose
Polysaccharides
 Macromolecules
consisting of many
monosaccharides
 Storage
and structure
 Function
depends on specific
monomers and their positions
Storage Polysaccharides
 Starch-
storage polysaccharide of plants
all glucose monomers
◦
◦
◦
◦
Joined by 1-4 linkages usually (similar to maltose)
Bond angle  helical shape
Amylose – simple, unbranched (1-4)
Amylopectin – more complex, branched (1-6)
 Plants
store surplus starch as granules
within chloroplasts and other plastids
LE 5-6a
Chloroplast
Starch
1 µm
Amylose
Amylopectin
Starch: a plant polysaccharide
Storage Polysaccharides

Glycogen- storage polysaccharide in
animals

Humans & other vertebrates store
glycogen in liver & muscle cells

Similar to amylopectin, more branched
LE 5-6b
Mitochondria Glycogen granules
0.5 µm
Glycogen
Glycogen: an animal polysaccharide
Structural Polysaccharides

Cellulose- major component of the tough
wall of plant cells

Like starch, cellulose is a polymer of
glucose, but the glycosidic linkages differ

The difference is based on two ring forms
for glucose: alpha () and beta ()
LE 5-7
a Glucose
b Glucose
a and b glucose ring structures
Starch: 1–4 linkage of a glucose monomers.
Cellulose: 1–4 linkage of b glucose monomers.
• α glucose = Hydroxyl above the ring
• β glucose = Hydroxyl below the ring
• Cellulose = β glucose
• Starch = α glucose
• In straight structures, H atoms on
one strand can bond with OH groups
on other strands
• Microfibrils: cable-like groups of
cellulose that maintain structural
integrity
LE 5-8
Cellulose microfibrils
in a plant cell wall
Cell walls
Microfibril
0.5 µm
Plant cells
Cellulose
molecules
 Glucose
monomer
 Enzymes
that digest starch by
hydrolyzing alpha linkages can’t
hydrolyze beta linkages in cellulose
 Cellulose = insoluble fiber
 Some microbes use enzymes to digest
cellulose
 Many herbivores, from cows to
termites, have symbiotic relationships
with these microbes
Brainstorming: What is a symbiotic
relationship? Can you think of other
examples? What other forms of symbiosis
do you know of?
Structural Polysaccharides






Chitin- structural polysaccharide,
exoskeleton of arthropods & cell walls of
fungi
Pure chitin is leathery
Similar in structure to cellulose
Contains nitrogen side-chain
Calcium Carbonate (CaCO3)
Chitin can be used as surgical thread
Lipids

Large biological molecules that do not
form polymers
Lipids

All lipids are hydrophobic

Three lipids that are most important for
biological processes
◦ Fats
◦ Phospholipds
◦ Steroids
Fats
 Function is to store energy
 Glycerol and fatty acids bonded
by
ester linkages
 Glycerol is a 3-carbon alcohol with a
hydroxyl group attached to each
carbon
 A fatty acid is a carboxyl group
attached to a long carbon skeleton
LE 5-11a
Fatty acid
(palmitic acid)
Glycerol
Dehydration reaction in the synthesis of a fat
Fats
Nonpolar (water creates hydrogen bonds
with itself and excludes the fat)
 Three fatty acids  triglyceride

LE 5-11b
Ester linkage
Fat molecule (triacylglycerol)
Fats
Fatty acids vary in length
 Saturated fatty acids – contain the
maximum number of hydrogen atoms
possible (no double bonds)
 Unsaturated fatty acids – contain double
bond(s), reducing the number of
hydrogen atoms

Saturated Fats



Saturated fatty acids  saturated fats
Animal fats; solid at room temperature
A diet rich in saturated fats may contribute to
cardiovascular disease through plaque deposits
LE 5-12a
Stearic acid
Saturated fat and fatty acid.
Unsaturated fats


Unsaturated fatty acids  unsaturated fats
Plant and fish fats use unsaturated; liquid at
room temperature (oils)
LE 5-12b
Oleic acid
cis double bond
causes bending
Unsaturated fat and fatty acid.
Phospholipids

Hydrophilic Head
◦ Glycerol
◦ Phosphate group

Hydrophobic tail
◦ Two fatty acids
LE 5-13
Choline
Phosphate
Glycerol
Fatty acids
Hydrophilic
head
Hydrophobic
tails
Structural formula
Space-filling model
Phospholipid symbol
Phospholipids
When added to water, phospholipids form
a bilayer structure
 Cell membranes are made of phospholipid
bilayers

LE 5-14
Steroids
Carbon skeleton with 4 fused rings
 Cholesterol - component in animal cell
membranes
 Although cholesterol is essential in
animals, high levels in the blood may
contribute to cardiovascular disease

Lipids - Review

How is the structure of a phospholipid
different from the structure of a
triglyceride?
Proteins
Proteins > 50% of the dry mass of most
cells
 Protein have many functions

◦
◦
◦
◦
◦
◦
◦
structural support,
storage
transport
cell communications
movement
Defense
Etc…
Enzymes


Protein that acts as a catalyst (speeds up
chemical reactions)
Enzymes can perform their functions repeatedly,
functioning as workhorses that carry out the
processes of life
LE 5-16
Substrate
(sucrose)
Glucose
Enzyme
(sucrose)
Fructose
Proteins
 Constructed
from amino acids
 Polypeptides are polymers of
amino acids
 Proteins made up of one or more
polypeptide
Amino Acid Monomers
Organic molecules with a carboxyl, an
amino group, and a side chain (R group) all
joined by an alpha carbon
 Only difference between amino acids is the
side chain
 Cells use 20 amino acids to make thousands
of proteins

LE 5-UN78
 carbon
Amino
group
Carboxyl
group
LE 5-17a
Glycine (Gly)
Alanine (Ala)
Valine (Val)
Leucine (Leu)
Isoleucine (Ile)
Nonpolar
Methionine (Met)
Phenylalanine (Phe)
Tryptophan (Trp)
Proline (Pro)
LE 5-17b
Polar
Serine (Ser)
Threonine (Thr)
Cysteine (Cys)
Tyrosine (Tyr)
Asparagine (Asn) Glutamine (Gln)
LE 5-17c
Acidic
Basic
Electrically
charged
Aspartic acid (Asp) Glutamic acid (Glu)
Lysine (Lys)
Arginine (Arg)
Histidine (His)
Are amino acid side chains that are
electrically charged hydrophilic or
hydrophobic? Why?
Amino Acid Polymers
 Amino
acids linked by peptide bonds
 Polypeptide - polymer of amino acids
 Polypeptides range in length from a
few monomers to > 1000
 Each polypeptide has a unique linear
sequence of amino acids
Amino Acid Sequence
Frederick Sanger
 Used digestive enzymes to break
polypeptides at specific places
 Searched for overlapping regions to
determine original sequence

Amino Acid Sequence

Determine the sequence of the polypeptide
based on the following fragments if it starts with
Ser and ends with Cys:
◦
◦
◦
◦
◦
◦
◦

SerLeuTyr
TyrCys
LeuTyrGlu
CysSerVal
GluLeuGlu
GluAspTyr
SerValCys
Answer:
SerLeuTyrGluLeuGluAspTyrCysSerValCys
Proteins
Functional protein - one or more
polypeptides folded into a unique shape
 Sequence of amino acids determines a
protein’s 3-D conformation
 Protein’s conformation determines its
function
 Ribbon models and space-filling models
can depict a protein’s conformation

LE 5-19
Groove
A ribbon model
Groove
A space-filling model
Four Levels of Protein Structure
Primary structure - sequence of amino
acids
 Secondary structure- found in most
proteins, consists of coils (α-helices) &
folds (β-sheets) in the polypeptide chain
 Tertiary structure- determined by
interactions among various side chains (R
groups)
 Quaternary structure- consists of multiple
polypeptide chains

LE 5-20
 pleated sheet
+H
3N
Amino end
Amino acid
subunits
 helix
Primary Structure
LE 5-20a
Amino end
Amino acid
subunits
Carboxyl end
Secondary Structure
Secondary Structure

Secondary structure - coils & folds result
from hydrogen bonds between repeating
constituents of the polypeptide backbone

Typical secondary structures are a coil
called an alpha helix & a folded structure
called a beta pleated sheet
LE 5-20b
 pleated sheet
Amino acid
subunits
 helix
Tertiary Structure
Tertiary Structure
Determined by interactions between R
groups, NOT interactions between
backbone constituents
 Possible interactions between R groups:
H-bonds, ionic bonds, hydrophobic
interactions, & van der Waals interactions
 Strong covalent bonds called disulfide
bridges may reinforce the protein’s
conformation

LE 5-20d
Hydrophobic
interactions and
van der Waals
interactions
Polypeptide
backbone
Hydrogen
bond
Disulfide bridge
Ionic bond
Quaternary Structure
Quaternary Structure
Two or more polypeptide chains that form
one macromolecule
 Examples

◦ Collagen is a fibrous protein consisting of 3
polypeptides coiled like a rope
◦ Hemoglobin is a globular protein consisting of
four polypeptides: two alpha & two beta chains
LE 5-20e
Polypeptide
chain
 Chains
Iron
Heme
Polypeptide chain
Collagen
 Chains
Hemoglobin
Protein Structure
Review Video
Sickle-Cell Disease
A slight change in primary structure can
affect a protein’s conformation and ability
to function
 Sickle-cell disease, an inherited blood
disorder, results from a single amino acid
substitution in the protein hemoglobin

LE 5-21a
10 µm
Red blood Normal cells are
cell shape full of individual
hemoglobin
molecules, each
carrying oxygen.
10 µm
Red blood
cell shape
Fibers of abnormal
hemoglobin deform
cell into sickle
shape.
LE 5-21b
Sickle-cell hemoglobin
Normal hemoglobin
Primary
structure
Val
His
1
2
Leu
Thr
3
4
Pro
Glu
5
6
Secondary
and tertiary
structures
7
 subunit
Quaternary Normal
hemoglobin
structure
(top view)
Primary
structure
Secondary
and tertiary
structures
Molecules do
not associate
with one
another; each
carries oxygen.
His
Leu
Thr
Pro
Val
Glu
1
2
3
4
5
6
7
Exposed
hydrophobic
region
 subunit

Quaternary
structure

Val


Function
Glu
Sickle-cell
hemoglobin


Function
Molecules
interact with
one another to
crystallize into
a fiber; capacity
to carry oxygen
is greatly reduced.


What Determines Protein
Conformation?
In addition to primary structure, physical
and chemical conditions can affect
conformation
 Change in pH, salt concentration,
temperature, or environmental factors can
cause denaturation
 Denaturation - loss of a protein’s native
conformation
 A denatured protein is biologically
inactive

LE 5-22
Denaturation
Normal protein
Denatured protein
Renaturation
The Protein-Folding Problem
It is hard to predict a protein’s
conformation from its primary structure
 Most proteins probably go through several
states on their way to a stable
conformation
 Chaperonins- protein molecules that
assist the proper folding of other proteins

LE 5-23a
Cap
Hollow
cylinder
Chaperonin
(fully assembled)
LE 5-23b
Polypeptide
Steps of Chaperonin
Action:
An unfolded polypeptide enters the
cylinder from one
end.
Correctly
folded
protein
The cap attaches, causing
the cylinder to change
shape in such a way that
it creates a hydrophilic
environment for the
folding of the polypeptide.
The cap comes
off, and the
properly folded
protein is released.
 Scientists
use X-ray
crystallography or nuclear
magnetic resonance to determine
a protein’s conformation
LE 5-24a
X-ray
diffraction pattern
Photographic film
Diffracted X-rays
X-ray
source
X-ray
beam
Crystal
LE 5-24b
Nucleic acid
X-ray diffraction pattern
3D computer model
Protein
Nucleic Acids
The amino acid sequence of a polypeptide
is programmed by a unit of inheritance
called a gene
 Genes are made of DNA
 DNA is made up of nucleotides

Nucleic Acids

Two kinds nucleic acids:
◦ Deoxyribonucleic acid (DNA)
◦ Ribonucleic acid (RNA)
DNA provides directions for its own
replication
 DNA directs synthesis of messenger RNA
(mRNA), which directs protein synthesis
 Protein synthesis occurs in ribosomes

LE 5-25
DNA
Synthesis of
mRNA in the nucleus
mRNA
NUCLEUS
CYTOPLASM
mRNA
Movement of
mRNA into cytoplasm
via nuclear pore
Ribosome
Synthesis
of protein
Polypeptide
Amino
acids
The Structure of Nucleic Acids

Monomers – nucleotides

Nucleic acids - polymers of nucleotides
(polynucleotides)

Nucleotide - nitrogenous base, pentose sugar,
and a phosphate group

Nucleotide without a phosphate group is a
nucleoside
LE 5-26a
5 end
Nucleoside
Nitrogenous
base
Phosphate
group
Nucleotide
3 end
Polynucleotide, or
nucleic acid
Pentose
sugar
Nucleotides
Nucleosides + phosphate groups
 Nucleoside = nitrogenous base + sugar
 Two types of nitrogenous bases:

◦ Pyrimidines are single 6-membered ring
 Cytosine, Thymine, Uracil
◦ Purines are 6-membered ring fused to a 5membered ring; double ring
 Adenine, Guanine
LE 5-26b
Nitrogenous bases
Pyrimidines
Cytosine
C
Thymine (in DNA) Uracil (in RNA)
U
T
Purines
Adenine
A
Guanine
G
Pentose sugars
Deoxyribose (in DNA)
Nucleoside components
Ribose (in RNA)
The DNA Double Helix




A DNA molecule has 2 polynucleotides
spiraling around an imaginary axis, forming a
double helix
Backbones run in opposite 5´ to 3´ directions
from each other; antiparallel
One DNA molecule has many genes –
combinations of nitrogenous bases
Nitrogenous bases in DNA form H-bonds
between complementary bases:
◦ Adenine and Thymine (or Uracil, in RNA)
◦ Guanine and Cytosine
LE 5-27
5 end
3 end
Sugar-phosphate
backbone
Base pair (joined by
hydrogen bonding)
Old strands
Nucleotide
about to be
added to a
new strand
5 end
New
strands
5 end
3 end
5 end
3 end
Biomolecule
Class
Atoms
present
Building
blocks
Lipids
MacroMolecule
CHO
Glucerol
& fatty
acids
Carbs
Polymer
CHO
Proteins
Polymer
Nucleic
Acids
Polymer
examples
Polymer
examples
Functions
Where
can be
found in
living
things
What is it?
Primary
Secondary
Tertiary
Quarternary
Chemical
bonds
involved
Draw it
Example