Chapter 5
The Structure and Function of
Macromolecules
Essential Ideas:
•Compounds of carbon, hydrogen and oxygen are
used to supply and store energy.
•Proteins have a very wide range of functions in
living organisms.
•The structure of DNA allows efficient storage of
genetic information.
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TOK
• There are conflicting views as to the
harms and benefits of fats in diets.
How do we decide between competing
views?
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TOK
• The story of the elucidation of the
structures of DNA illustrates that
cooperation and collaboration among
scientists exist alongside competition
between research groups. To waht
extent is research in secret “antiscientific”?
• What is the relationship between
shared and personal knowledge in the
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natural world?
Macromolecules
• There are many molecules that comprise
living organisms and many of them are quite
large.
• As such, they are called macromolecules.
• There are 4 main macromolecules that
comprise living organisms:
– 1. Proteins.
– 2. Lipids.
– 3. Carbohydrates.
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– 4. Nucleic acids.
Macromolecules
• Three of the four classes
(carbohydrates, protein, and nucleic
acids) are comprised of polymers which
are long molecules made up of the
same or similar subunits covalently
linked together.
• The subunits that are linked together
are called monomers.
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Macromolecules
• The synthesis and breakdown of
macromolecules is governed by a
series of condensation/dehydration or
hydrolysis reactions.
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Condensation Reactions
• In a condensation reaction (aka a
dehydration reaction) monomers are
added to a growing polymer and a
water molecule is given off--hence the
name dehydration reaction.
• These reactions require energy and the
action is carried out by enzymes.
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Hydrolysis
• Hydrolysis is the process that adds a water
molecule to a polymer giving one of the
monomers.
• This occurs during digestion and it makes the
large molecules useable by our bodies by
producing smaller subunits that our cells can
uptake.
• The four main types of macromolecules can
be broken down further and analyzed.
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Carbohydrates
• Carbohydrates are molecules
consisting of carbon, hydrogen, and
oxygen.
• The three classifications are
monosaccharides or simple sugars,
disaccharides or double sugars, and
polysaccharides which are 3 or more
sugars linked together forming a sugar
polymer.
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Monosaccharides
• Monosaccharides generally have the
formula CnH2nOn and depending on the
location of the carbonyl group, the
sugar is either an aldose or a keytone.
• When the carbonyl group is the last
carbon on the chain, it is an aldose,
when it is not, it is a keytone.
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Monosaccharides
• Glucose C6H12O6 is an aldehyde that is
a common monosaccharide used as
energy by our body.
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Monosaccharides
• Not only is it used as an energy energy
source (as are other monosaccharides),
but their carbon skeletons serve as
building blocks for other major
macromolecules within the organism-amino acids and fatty acids.
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Disaccharides
• A disaccharide, such as sucrose,
lactose, and maltose are joined
together by a glycosidic linkage--a
covalent bond between 2
monosaccharides by a dehydration
reactions.
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Disaccharides
• The fruit of a plant is often a great
source of sucrose--glucose and
fructose (the most common
disaccharide) because as the plants
form it during photosynthesis, this is
where it gets stored.
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Disaccharides
• Other common disaccharides include
lactose and maltose.
• Lactose = milk sugar.
• Maltose = formed from the breakdown
of starch by amylase.
http://en.wikipedia.org/wiki/Lactose
http://en.wikipedia.org/wiki/Maltose#mediaviewer/File:Maltose2.svg
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Polysaccharides
• When monosaccharides are
glycosidically linked together thousands
of times, polysaccharides are formed.
• There are 2 main types of
polysaccharides, structural and storage.
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Structural or Storage?
• There are actually 2 forms of glucose, 
and , and the form is determined by
the placement of a hydroxyl group.
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Structural or Storage?
• In  -glucose, the -OH group is below
the ring structure and in -glucose, it is
above the ring structure.
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Structural Polysaccharides
• In structural
polysaccharides,
strong materials
are built to provide
strength and
support for the
organism.
• A good example of
this is cellulose.
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Structural Polysaccharides
• Plant cell walls are comprised of
cellulose which gives them strength.
Some animals such as cows can digest
cellulose, but humans can’t.
• For us, it is called “insoluble fiber” and
is found in many fruits and vegetables.
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Structural Polysaccharide
• Another important structural polysaccharide
is chitin.
• Chitin makes up the hard exoskeleton of
arthropods, and the cell walls of fungi.
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Storage Polysaccharides
• Although the starch and cellulose
molecules are comprised of glucose
molecules, the different types of
glucose give them vastly different uses.
• For example starch can be used by
humans for food, cellulose can’t.
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http://en.wikipedia.org/wiki/Amylose#mediaviewer/File:Amylose2.svg
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Amylose and Amylopectin
• Starch is comprised of two components:
amylose and amylopectin.
– Amylose comprises 20-30% of the structure
and is more resistant to digestion.
– Amylopectin makes up 70-80% of a starch
molecule and is more easily digested.
http://en.wikipedia.org/wiki/Amylose
http://en.wikipedia.org/wiki/Amylose#mediaviewer/File:Amylose2.svg
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Storage Polysaccharides
• There are two main
types of storage
polysaccharides:
That which is found
in plants (starch),
and that which is
found in animals
(glycogen).
• Glycogen is
branched, and
starch is helical.
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Proteins
• Proteins are another
class of
macromolecules
consisting of many
monomers linked
together by peptide
bonds forming
polymers.
• Enzymes are protein
polymers that act as
catalysts within cells.
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Proteins
• Polymers of amino acids are called
polypeptides and the same 20 amino acids
form all polypeptides.
• Proteins consist of one or more of the
polypeptides coiled into a specific
conformation.
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Proteins
• Amino acids are
organic molecules
containing a
carboxyl group and
an amino group.
• These are each
bounded to a
central carbon
atom which also
has an amino acid
attached to it.
 carbon
Amino
Group
Carboxyl
Group
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Proteins
• There are 2 groups that are linked
together to form a peptide bond.
• A peptide bond is a dehydration
reaction which links the amino group of
one amino acid to the carboxyl group of
a different amino acid yielding water in
the process.
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Proteins
• Once amino acids are added to the
polypeptide, they begin to interact with
the other amino acids on the growing
polypeptide.
• The sequence then determines the 3D
conformation the protein will take.
• The conformation of the protein
determines how it will function.
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Proteins
• An enzyme is an example and the
conformation it takes determines how it
functions when it interacts with a
substrate.
• There are 4 different types of protein
structure: 1°, 2°, 3°, and 4°.
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Proteins--Primary Structure
• The primary structure
is the specific
sequence of amino
acids.
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Proteins--Primary Structure
• Proteins
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Proteins--Primary Structure
• Primary Structure
• The order of the amino acids.
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Proteins--Secondary
Structure
• The secondary structure of the polypeptide is the
coiled and/or folded patterns that emerges as the
amino acids begin to interact with one another (Hbonds) not from the R-groups, but from the
backbones of the amino acids.
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Proteins--Secondary
Structure
• Secondary Structure
• The folding configuration.
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Proteins--Secondary
Structure
• There are two main types of secondary
protein structure, the  -helix and the pleated sheet.
• The  -helix is a delicate coil held
together by H-bonds.
• The -pleated sheet forms when 2
polypeptides are aligned side by side
and hydrogen bond along their lengths.
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Proteins--Tertiary Structure
• The tertiary
structure of the
protein is due to
the interactions of
the R-groups on
the amino acids.
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Proteins--Tertiary Structure
• Tertiary Structure
• R-group interaction.
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Proteins--Quaternary
Structure
• The quaternary structure of a protein occurs
when 2 or more polypeptide chains interact
with each other to form a large, functional
protein.
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Proteins--Quaternary
Structure
• Quaternary Structure
• The final, finished protein.
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Your Proteome
• We know that proteins are coded for by our
genes.
• Each individual has a unique set of genes
that code for each protein in your body.
• Thus, your proteome is unique to you. While
you code for the same proteins as all other
human beings, the minor differences we have
is what make us all different.
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Small Change = Big
Problem
• Sickle cell anemia
example: glutamic
acid out, valine in,
causes changes in
quaternary structure.
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Nucleic Acids
• Nucleic acids store and
transmit information about a
protein’s primary structure.
• There are 2 types of nucleic
acids: RNA and DNA.
• DNA provides the necessary
information for guiding its
own replication.
• It also guides RNA synthesis
and using RNA controls
protein synthesis.
QuickTime™ and a
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Nucleic Acids
• DNA is the information that controls the
cell. This information is used to create
messenger RNA that interacts with the
cells protein synthesizing machinery
(ribosomes) to create the proteins that
run the cell.
• DNA--> RNA --> Protein
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Nucleic Acids
• Nucleic acids are
polymers called
polynucleotides which
consist of monomers
called nucleotides.
• The nucleotides are
composed of a
pentose (a 5-carbon
sugar), a nitrogenous
base, and a
phosphate group.
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Nucleic Acids
• The nucleotide
monomers are built
from sugar atoms
(ribose and
deoxyribose) attached
to a nitrogenous base
(C,T, U, A G). This
forms a nucleoside
which becomes a
nucleotide once the
phosphate group has
been added.
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Nucleic Acids
• Nucleotides are linked together by covalent
(phosphodiester) bonds between a hydroxyl
group on the 3’ carbon of one nucleotide and
the phosphate on the 5’ carbon on the next.
• This bond starts the repeating sugarphosphate bond. This gives rise to the 3’ and
5’ ends of the DNA molecule. The sequence
of each of the bases in the polynucleotide is
unique to each gene.
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Nucleic Acids
• RNA consists of a single strand of
nucleic acids in a polynucleotide chain.
• DNA, on the other hand, consists of 2
polynucleotide chains that run in
opposite directions to one another.
• This gives rise to the term “antiparallel.”
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Nucleic Acids
• The 2 anti-parallel strands of DNA
appear like a divided highway and are
joined together by hydrogen bonds and
Van der Waals interactions.
• H-bonds are between paired bases
• Van der Waals interactions are between
stacked bases.
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Nucleic Acids
• There are certain bases that you find in
DNA and RNA.
• DNA has A,T,C,G
• RNA has A,U,C,G
• When the bases pair together, they only
pair one way: A & T, C & G in DNA, and
in RNA A pairs with U, C pairs with G.
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Nucleic Acids
• The two strands are always said to be
complementary. That is, if you know
the order of one strand of DNA, you can
deduce the other.
• 5’ --------> 3’
• AGGTCCG
• TCCAGGC
• 3’<-------- 5’
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Nucleic Acids
• This feature of DNA is what makes
precise copying possible.
• When cells divide, the DNA serves as a
template and the new DNA that is
formed is copied from it.
• When finished, there are 2 identical
copies (ideally) of DNA within the cell
and identical daughter cells can now
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form upon division.
Nucleic Acids
• The parts of the DNA molecule that
make up the polynucleotides that
encode for the amino acids can be used
to show how closely organisms are
related from an evolutionary standpoint.
• Molecular biologists can sequence
genes and determine how much
difference there is between organisms
and this helps them form their tree of
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life.
Nucleic Acids
• For example, upon examination of the
polypeptide chain of human hemoglobin
with that of a gorilla, we only find one
amino acid different out of 146.
• In gibbons, which are a tree monkey
found in SE Asia, there is only a
difference of 2 amino acids.
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Lipids
• There are three classes of lipids:
• Fats (Fatty acids)
– Saturated
– Monounsaturated
– Polyunsaturated
• Phospholipids
• Steroids
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Lipids
• Lipids are not
polymers, they are
long chain fatty
acids attached via
a dehydration
reaction to a
glycerol head.
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Lipids
• Triglycerides are formed from the
condensation of three fatty acids and
one glycerol.
http://science.halleyhosting.com/sci/ibbio/chem/notes/chpt3/triglyceride.htm
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Lipids
• Lipids
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Lipids
• The glycerol molecule is a 3 carbon
alcohol with a hydroxyl group attached
to each carbon. During the reaction,
the carboxyl group at the end of the
fatty acid loses its hydroxyl (-OH) and
attaches to the oxygen on the glycerol
molecule. The -H lost from the glycerol
combines with the -OH forming water.
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Lipids
• The fatty acid portion is a long
hydrocarbon usually 16 to 18 carbons in
length.
• These portions are hydrophobic and
this makes fats hydrophobic.
• Fatty acids can be classified as
saturated or unsaturated--as we often
hear about in nutrition.
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Lipids
• When they are saturated, all
of the carbon atoms contain
a maximum number of H
atoms n the chain. Thus
they are allowed to group
tightly together as we see in
butter and animal fat. Most
animal fat is saturated.
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Lipids
• Unsaturated fats contain carbon atoms
that are double bonded to other carbon
atoms in the fatty acid chain. This
creates a kink in the chain and prevents
the molecules from packing closely
together.
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Lipids
• Such examples are
olive oil and
vegetable oil.
• The oils of fish and
vegetables
generally are
unsaturated.
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Lipids
• Lipids are normally used for long-term
energy storage.
• Carbohydrates are short-term energy.
• Lipids are stored in adipose tissue.
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Lipids
• Why lipids?
– Lipids store twice the amount of energy as
proteins and carbohydrates.
• 1 gram fat = 9 calories
• 1 gram protein = 4 calories
• 1 gram carbohydrate = 4 calories
– Compared to carbohydrates, lipids add
only ⅙ as much body mass as
carbohydrates.
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Lipids
• Why lipids?
– Fats are stored as pure fat droplets whereas
glycogen is associated with water.
(energy in) 1g lipids
– Mass used for storage =
(energy in) 2g carbs + 4g associated H2O
– =⅙
– This is critical for active animals that need to carry
their energy stores--bats and birds and the like.
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Lipids Vs. Glycogen
• There is a tradeoff between glycogen
and lipids.
• Lipids are lighter to carry, but glycogen
can be mobilized faster.
• Glycogen is rapidly broken down and
glucose is made available to cells
quickly via the bloodstream.
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Saturated
• Saturated fats have the maximum
amount of hydrogens attached to the
carbon tails.
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http://www.agricultured.org/fats-in-food/
Saturated Fats
• Saturated fats are solid at room
temperature.
• They are found in animal products like
butter, cheese and milk.
• Palm oil and coconut oils are also high
in saturated fats, but are exceptions to
the “solid at room temperature” rule of
thumb.
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Monounsaturated
• Monounsaturated fats have one C-C
double bond.
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http://www.agricultured.org/fats-in-food/
Monounsaturated Fats
• Monounsaturated fats are found in plant
based oils such as olive, canola, and
soybean oil.
• Fish, nuts, seeds, and some vegetables
are rich in monounsaturated fatty acids.
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Polyunsaturated
• Polyunsaturated fats have multiple C-C
double bonds.
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http://www.agricultured.org/fats-in-food/
Polyunsaturated Fats
• Polyunsaturated fats are commonly
referred to as omegas.
• Omega-3 and Omega-6 are common
examples.
• Corn, soybean, safflower oils are
common sources of Omega-6.
• Soybean and canola oils, walnuts,
flaxseed and fish are common sources
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of Omega-3.
Cis-Unsaturated Fats
• “Cis-” means, “same side.” This means
that the hydrogens are on the same
side of the double bond in the C-C
double bond.
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http://www.agricultured.org/fats-in-food/
Trans-Unsaturated Fatty
Acids
• “Trans-” means “opposite.”
• This means that the hydrogens are on
the opposite sides of the C-C double
bond.
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http://www.agricultured.org/fats-in-food/
Trans-Unsaturated Fatty
Acids
• Most trans fats are artificially produced
by a process called hydrogenation-where extra hydrogens are added to
unsaturated fats.
• Many trans fats have a straightened
shape that makes them ideal for the
food industry.
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Trans-Unsaturated Fatty
Acids
• They are not “saturated fats,” but
behave like them.
• They make margarine buttery, yet soft.
• They give Crisco its properties.
• They make things such as Jif peanut
butter stay solid at room temperature.
• Most food companies have recently
taken trans-fats out of their products.
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Health Risks Associated
with Trans & Saturated Fats
• There have been many claims about the
effects of different types of fats on human
health.
• The main risk factor associated with
these fats is that of coronary heart
disease.
• In this disease, coronary arteries become
partially or completely blocked by fatty
deposits leading to heart attacks. 88
Health Risks Associated
with Trans & Saturated Fats
• A positive correlation has been found
between saturated fat intake and rates
of CHD in many studies.
• Correlation ≠ causation.
• A lowered fiber intake could be
responsible.
• Maasai of Kenya have a diet rich in
meat, fat, blood and milk--thus a high
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consumption of saturated fats.
Health Risks Associated
with Trans & Saturated Fats
• CHD is almost unheard of in the Maasai
population.
• Diets rich in olive oil and other cismonounsaturated fatty acids are
traditionally eaten in countries around the
Mediterranean. These countries
populations typically have low rates of
CHD.
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• Genetic factors could also be responsible.
Health Risks Associated
with Trans & Saturated Fats
• Other aspects of the diet could also be
responsible for CHD rates.
• There is a positive correlation between the
amount of trans-fat consumed and rates of
CHD.
• Other risk factors have been tested to see
if they account for the correlation; none did.
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Health Risks Associated
with Trans & Saturated Fats
• Trans-fats are probably responsible for
CHD.
• In patients who died from CHD, fatty
deposits in the diseased arteries were
found to contain high concentrations of
trans-fats.
• This lends more evidence to the causal
link.
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Determination of BMI Using
a Nomogram
• Body Mass Index (BMI) is a tool used to
screen individuals for possible weight
problems.
BMI
Below 18.5
18-6-24.9
25.0-29.9
30.0 and Above
Status
Underweight
Normal
Overweight
Obese 93
Determination of BMI Using
a Nomogram
• BMI =
mass in kilograms
(height in meters)2
• The units for BMI are kg/m2
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Determination of BMI Using
a Nomogram
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Determination of BMI Using
a Nomogram
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Phospholipids
• Phospholipids are a very important
molecule that are similar to fact except
that they only have 2 fatty acids
attached to the glycerol head.
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Phospholipids
• The 3rd carbon is
attached to a
phosphate group.
The phosphate
group has a
negative charge
and allows the
phospholipid to be
both hydrophobic
and hydrophilic.
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Phospholipids
• The head region of the phospholipid is hydrophilic
and the tail region of the phospholipid is
hydrophobic.
• Thus, when phospholipids are added to water they
form a bilayer with the heads orienting out, in contact
with the water and the tail regions are pointing
inward away from the water.
• This forms the basis of the phospholipid bilayer that
is the cell membrane.
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Steroids
• Steroids are a final class of lipids that
we’ll discuss. They are comprised of 4
fused rings and have various functional
groups attached to them.
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Steroids
• Cholesterol is an important sterol found
in animal cell membranes and is the
precursor of many hormones found
within the body.
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Steroids
Testosterone
Estrogen
Cortisol
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