Lecture 4: Biological

Molecules

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 In this
•
lecture…
Macromolecules
– Monomers and polymers
• The four classes of biological molecules
– Lipids
• Saturated, unsaturated, trans fats
• Phospholipids
• Steroids
– Carbohydrates
• Monosaccharides, disaccharides, polysaccharides
– Proteins
• Amino acids
• Primary, secondary, tertiary, quarternary structure
– Nucleic acids
• Nucleotides
• DNA and RNA
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 The four classes of
biological
• All living things aremolecules
made up of four classes of
large biological molecules: carbohydrates, lipids,
proteins, and nucleic acids
• These are macromolecules - large molecules
composed of thousands of covalently
connected atoms
• Molecular structure dictates “Macro”
=
function
All four classes are organic molecules! “large”

Not all organic molecules are part of one of

the four classes of biological molecules!

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What do macromolecules look
like?

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 What do they
do?
Type of macromolecule Example Function
Lipids Fat Cell membranes, energy
storage
Carbohydrates Starch, sugar Energy
storage,
structure
Nucleic acids DNA, RNA Store genetic material
Proteins Trypsin Cell machinery

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• Polymer - a long molecule consisting of
many similar building blocks
• Monomer – the building block
• Three of the four classes of life’s organic
molecules are polymers
– Carbohydrates
– Proteins
– Nucleic acids

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 Polymers and
monomers
(of both nonbiological type)

Monomer

Polyme
r

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Polymers and
monomers
(of the nonbiological type)

Nylon
monomer

Nylon A monomer is a
polymer single pattern
repeated over and
over. It can be
composed of many
atoms

Nylon
polymer

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 Kevla
r

Polyethylen
e

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Creating and breaking down
polymers
• Dehydration/condensation reaction - two
monomers bond together through the loss of a
water molecule
• Hydrolysis – two bonded monomers split apart
using a water molecule

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Figure 5.2
(a) Dehydration reaction: synthesizing a
polymer

1 2 3
Short polymer Unlinked
monomer

Dehydration
removes a water
molecule, forming a
1 bond.
new 2 3 4
Longer
polymer
(b) Hydrolysis: breaking down a
polymer
4
1 2 3

Hydrolysis adds
a water
molecule,
breaking a bond.

1 2 3
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BIOL 211 Spring 12
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 Class I:
Carbohydrates
• Sugars and the polymers of sugars
• Simplest carbohydrate monomers are
monosaccharides
• More complex carbohydrate polymers are
called
polysaccharides
• Purpose: fuel and fuel storage, building
material
– Sugar
– Cellulose BIOL 211 Spring
2012
13
 Examples of
• carbohydrates
Sugar, starch, cellulose,
glucose

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 Sugar Carbo =
carbon,

•
s Hydrate =
water
Monosaccharides have molecular formulas that
are usually multiples of CH2O
• Glucose (C6H12O6) is the most
common monosaccharide
• Monosaccharides are classified by
– The location of the carbonyl group (as aldose
or ketose)
– The number of carbons in the carbon skeleton
• 3, 5, or 6 carbons

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 Structure of
• carbohydrates
Composed of carbon, hydrogen, and
oxygen
• Though often drawn as linear skeletons,
in aqueous solutions many sugars form
rings

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Figure 5.3
Aldoses (Aldehyde Sugars) Ketoses (Ketone
Sugars)
Trioses: 3-carbon sugars (C3H6O3)

Glyceraldehyde Dihydroxyacetone

Pentoses: 5-carbon sugars (C5H10O5)

Ribos Ribulose
e
Hexoses: 6-carbon sugars
(C6H12O6)

Glucose Galactose Fructose

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 Figure 5.4

1 6 6
2
5 5
3
4 1 4 1
4
2 2
5 3 3

(a) Linear and ring

forms

6
5
4 1
3 2

( c ) C0h12air
(b) Abbreviated ring BIOL 211 Sp ir n g2 18
structure
 Monosaccharide
• s carbohydrate monomers…
Some common
– Fructose
• Fruit sugar
– Glucose
• Produced by photosynthesis, used as energy
storage
– Ribose
• Important in RNA (ribonucleic acid)

Glucos
e
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 High fructose corn
• syrup
Primary sweetener in the U.S. due to
corn subsidies and foreign sugar tariffs
• FDA says GRAS, but still health concerns on
the rise
• Normal corn syrup is all glucose
– Enzymatic processing converts glucose into
fructose
• HFCS is 24% water, the rest sugar
– 55% fructose, 45% glucose HFCS used in soda
– Fructose is much sweeter than glucose
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Two forms of glucose: alpha () and beta
()
• Cis-trans
isomers

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 2

Disaccharide
• s
Two monosaccharides bond together using a
dehydration reaction to create a
disaccharide
– The bond between two monosaccharides is
called a
glycosidic bond
• Examples of disaccharides:
– Sucrose
• Table sugar
– Lactose
• Sugar found in milk
– Maltose
• The enzyme amylase breaks down starch to produce
maltose BIOL 211 Spring
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A glycosidic bond/linkage joins a carbohydrate to another group, which may
or may not be another carbohydrate

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 Lactose
intolerance

• Inability to digest the sugar in milk

• Caused by a lack of the enzyme lactase, which
hydrolyzes lactose into its monosaccharides
glucose and galactose
• Bacteria in your gut can metabolize it through
fermentation though, which produces
hydrogen, carbon dioxide, and methane

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 Sucrose intolerance is a rare metabolic disorder
characterized by the lack of ability to break down
the disaccharide sucrose

-What sort of diet would someone with sucrose intolerance have to

follow?
-What happens if someone with sucrose intolerance were to eat
something containing sugar?

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 Man
y
Polysaccharide
• s
Many monosaccharides linked
together through glycosidic bonds
• The structure and function of a
polysaccharide are determined by its sugar
monomers and the positions of glycosidic
bonds
• Two types of polysaccharides: storage
and structural

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 Examples of
• polysaccharides
Storage
– Starch
• Two types of plant starches: amylopectin and
amylose
– Glycogen
• Branched chains of glucose found in animals

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 Storage
• polysaccharides
Starch, a storage polysaccharide of plants,
consists entirely of glucose monomers
joined by glycosidic bonds
• Stores energy in the potential chemical
energy in the bonds of carbohydrates
– Plants store surplus starch as granules
within organelles as amylose and
amylopectin
– Animals also store starch in the form of
glycogen in liver and muscle cells
• The simplest form of starch is amylose
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Figure 5.6

Chloropla Starch
st granules Amylopecti
n

Amylose
(a) Starch: 1
a plant m
polysaccharide
Mitochondria Glycogen
granules

Glycogen
(b) 0.5
an animal
Glycogen: m BIOL 211 Spring 29
polysaccharide 2012
 Structural
polysaccharides
• The polysaccharide cellulose is a 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 ()

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BIOL 211 Spring 31
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 Polymers with Polymers with
 glucose  glucose
are helical are straight

• In straight structures, H atoms on one strand can

hydrogen
bond with OH groups on other strands
• Parallel cellulose molecules held together this way
are grouped into microfibrils, which form strong
building materials for plants

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Why is  glucose used in
cellulose?

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 What is
• fiber?
Enzymes that digest starch by hydrolyzing 
linkages can’t hydrolyze  linkages in cellulose
• Cellulose in human food passes through the
digestive tract as insoluble fiber
• Some microbes use enzymes to digest cellulose
• Many herbivores, from cows to termites,
have symbiotic relationships with these
microbes

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 Structural
polysaccharides
• Chitin is in the
exoskeleton of
arthropods and
the cell walls of
many fungi

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 What are the two main types of
polysaccharides? What are some examples
of each?

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 Class
• 2:that does not form polymers
The only class
• Lipids are hydrophobic because they consist
mostly of hydrocarbons, which form
nonpolar covalent bonds
• The most biologically important lipids are
fats, phospholipids, and steroids
• Purpose: fuel storage, cell membranes

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 Examples of
• lipids
Oils, fats, phospholipids,
steroids

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 Fat
• Two components: glycerol and 3 fatty
acids
s
• The major function of fats is energy
storage
carbon alcohol with a A fatty acid consists of a
hydroxyl group carboxyl group attached to
attachedisto
Glycerol each
a three- a long carbon skeleton
carbon

The hydrogen on this hydroxyl group can

“pop” off in water. Since the molecule is
donating a hydrogen, it is classified as an
acid

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Synthesis of
fats In a fat, three fatty acids are
joined to glycerol by an
ester linkage

Generic ester functional group

form:

=
O
R’ - C – O – C – R’

This creates a
triacylglycerol,
AKA triglyceride

In cooking, fats break apart into

smaller molecules that produce
the characteristic “deep fried”
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• Fatty acids vary in length (number of carbons)
and in the number and locations of double
bonds
– Usually 4-35 carbons long
• Saturated fatty acids have the maximum
number of hydrogen atoms possible and no
double bonds
– Each carbon ‘saturated’ with hydrogens
• Unsaturated fatty acids have one or more
double bonds

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Saturated
fats The straight hydrocarbon
chains “stack” very
closely together

(Think of
straight
pencils in
a box)

Because they are so

densely packed,
saturated fats tend to
be solid at room temp

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 Unsaturated
• Fats
Includes polyunsaturated
and monounsaturated
fats on nutrition labels

The double bond “kinks” the

hydrocarbon chain and forces it
to bend

The hydrocarbon chains

don’t stack so easily,
and so are less dense.
Unsaturated fats tend to
be liquid at room temp

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 Polyunsaturated and Monounsaturated
•Fats
Monounsaturated fats have only one carbon-carbon
double bond
• Polyunsaturated fats have two more more carbon-
carbon double bonds
• Certain unsaturated fatty acids are not synthesized in
the human body, and must be supplied in the diet
• These essential fatty acids include the omega-3 fatty
acids, required for normal growth, and thought to
provide protection against cardiovascular disease

Poly =
many
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Mono = 2012
 Saturated
fat

The fatty acid tails

can freely rotate
around the glycerol
head
Monounsaturated
fat

Polyunsaturated
fat

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 Trans
•
fats
Produced by artificially saturating unsaturated fats by
adding hydrogen – “hydrogenation”
– Nickel is added to unsaturated liquid oil as a catalyst
– The mix is exposed to high temperature and pressure as hydrogen
gas is pumped through
– Nickel is filtered out
• Hydrogenation also straightens the kinks in unsaturated
fats, isomerizing from cis to trans form
CH3
Cis form

Pentene
CH3
Trans
form
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 Why hydrogenate
• fats?
Saturated fats tend to be solid at room temp
– In baked goods, saturated fats produce a much
better “mouth feel” and texture than unsaturated
fats
– Cheaper to hydrogenate the polyunsaturated fats in
vegetable oil than acquire natural saturated fats
from animal sources
• Saturated fats are more stable than unsaturated
fats
– Beef has a longer shelf life than pork or chicken because
it has a larger proportion of saturated fats
• Partially hydrogenated vegetable oil: some of the
carbon-carbon doubleBIOLbonds
211 Spring are hydrogenated, 49
2012
 Why so bad for
you?
Why are saturated fats so bad for you
vs. unsaturated fats? Why are trans
fats
particularly unhealthy?

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 Why so bad for
you?
“A group of identical and regular molecules fits together more neatly
than different and irregular molecules”

Triglycerides circulate in your blood. Saturated and trans fats

clump together much more easily in your blood vessels,
forming plaque that blocks arteries

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 Phospholipid
• s are the major component of
Phospholipids
all cell membranes
• Four components: glycerol, phosphate
group, choline, 2 fatty acids
• The two fatty acid tails are hydrophobic,
but the phosphate, glycerol, and choline
form a hydrophilic head
– The entirety of a fat molecule is hydrophobic

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 The smell of bruised
leaves and cucumbers
both come from
phospholipid
fragments

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Phospholipids: the secrets of cell
membranes

• When added to water, phospholipids self-

assemble into a bilayer, with the hydrophobic
tails pointing toward the interior

• The structure of phospholipids results in a

bilayer arrangement BIOL
found
211 Springin cell membranes 54
2012
The notothenoids are a type of bony fish living in
Antarctica. The waters they inhabit range from -2C
to 4C. What would you expect the composition of
their cell membranes to be like?

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Phospholipids in drug
delivery • A big problem in medicine
is how to get drugs inside
Outside the cells where they can then
cell act

• Phospholipids can be coaxed

to form a hollow droplet
called a “liposome”

• Liposomes are filled with a

drug of interest

• Phospholipid liposomes merge

Inside the smoothly with the
cell phospholipid cell wall,
depositing their contents into
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 Phospholipids in
• The smellfood
of bruised leaves and cut
cucumbers comes from phospholipid
fragments
• Eggs are an abundant source of the
phospholipid lecithin
– Eggs are used to produce stable mixtures of fats
and water
• Mayonnaise
• Custards
• Hollandaise sauce
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 Eggs are an abundant source of the
phospholipid lecithin, and also a crucial
ingredient in mayonnaise, a smooth blend of
fat and water.
How do eggs contribute to the smooth blending
of fat and water?

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 Steroid
• s characterized by a
Steroids are lipids
carbon skeleton consisting of four fused
rings
• Cholesterol, an important steroid, is
a component in animal cell
membranes

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 Cholesterol: not such a bad
• guy?
Too much cholesterol can damage cell
walls and cause atherosclerosis
• Cholesterol stiffens animal cell
membranes
– OH group interacts with polar region, cyclic
rings embed within nonpolar region
– Cholesterol draws fatty acid chains together,
more densely packing phospholipids and
stiffening cell membranes

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Cholesterol as a chemical
precursor
Cholesterol

Enzymatic
reactions

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 Birth control
pills

If an egg has been fertilized, estrogen and progesterone levels remain

high

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 Steroids in
• medicine
Corticosteroids: used to treat a huge array
of diseases and symptoms
• Anabolic steroids: mimic the effect of
testosterone
– Increase the rate of protein synthesis in cells
– Result in increased muscle mass and secondary
sex characteristics
– Excess testosterone converted to estradiol,
which causes gynomastia in men
– Natural testosterone synthesis is suppressed,
resulting in testicular atrophy and reduced sperm
production BIOL 211 Spring 63
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 Class 3: Proteins

Proteins are important molecules in

cells. Proteins are the major
component of the dry weight of cells.
The name protein is derived from
a Greek word Proteios which means
pre-eminent or first. This name was
fist suggested in 1838 by a Swedish
chemist Berzelius. He suggested it to
a Dutch chemist Mulder and he
referred it to the complex organic
Proteins are the most abundant
intracellular macro-molecules.
Proteins are connected intimately
with all chemical and physical
activity, which constitutes the life of
the cell. Proteins are present in and
vital to all living cells. They provide
structure, protection to the body of
multicellular organism in the form of
skin, hair, callus, cartilage, ligaments,
 What are
Proteins?
Proteins are known as building
blocks of life.
Proteins are biomolecules, usually
large in size, that consists of one or
more chains of amino acids. Proteins
perform variety of functions
like catalyzing metabolic reactions,
replication of DNA, response to
stimuli, and transporting molecules.
Proteins differ from each other
 Characteristics
of Proteins
General Characteristics of Proteins
are as follows:
Proteins are organic substances,
they are made up of nitrogen and
also, oxygen, carbon an d hydrogen.

Proteins are the most important

biomolecules, they are the
fundamental constituent of the
cytoplasm of the cell.
 Properties of
Proteins
The general properties of proteins
are similar to those of the amino
acids:
 Physical
Properties of
Proteins
Proteins are colorless and tasteless.

They are homogeneous and

crystalline.

Proteins vary in shape, they may be

simple crystalloid structure to long
fibrilar structures.

Protein structures are of two distinct

 Chemical
Properties of
Proteins
Proteins when hydrolyzed by acidic
agents, like conc.HCl yield amino
acids in the form of their
hydrochlorides.

Proteins when are hydrolyzed with

alkaline agents leads to hydrolysis of
certain amino acids like arginie,
cysteine, serine, etc., also the optical
activity of the amino acids is lost.
 Protein
Classification
Classification of Proteins Based
on Shape

They are grouped under two

categories globular and fibrous.
 Globular or
Corpuscular
Proteins
Globular proteins have axial ratio
less than 10. They are compactly
folded and coiled. and possess a
relatively spherical or ovoid shape.
They are usually soluble in water and
in aqueous media. Example Insulin,
plasma albumin, globulin enzymes.
 Fibrous or Fibrillar
Proteins
These proteins have axial ratio more
than 10, hence, they resemble long
ribbons or fibres in shape. They are
mostly found in animals, and are not
soluble in water or in solution of
dilute acids. Fibrous proteins aid in
protection and structural support.
Example: Collagen, Keratin, Elastins,
Fibroin.
 Classification of
Proteins Based
Simpleon Composition
Proteins or Holoproteins
These proteins are made of only one
and Solubility
type of amino acid, as structural
component, on decomposition with
acids, they liberate constituent
amino acids. They are mostly
globular type of proteins except for
scleroproteins, which are fibrous in
nature.
Simple proteins are further
 Classification of
Proteins Based
on -Composition
Albumins They are widely
distributed in nature, mostly seen in
and Solubility
seeds. They are soluble in water and
dilute solutions of acids, bases and
salts. Example: Leucosine,
legumeline, serum albumin.

Globulins - They are of two types,

pseudoglobulins which are soluble in
water, other is euglobulins which are
 Conjugated or
Complex Proteins
Theseor
areHeteroproteins
proteins that are made of
amino acids and other organic
compounds. The non-amino acid
group is termed as prosthetic group.

Complex proteins are further

classified based on the type of
prosthetic group present.

Metalloproteins - These are proteins

 Classification of
Proteins on
Biological
Proteins depending upon their
physical and chemical structure and
Function
location inside the cell, they perform
various functions. Proteins are
grouped as follows, based on their
metabolic function they perform.

Enzymic Proteins
They are the most varied and highly
specialized proteins with catalytic
 Structure of
Proteins
There are four structural levels of
organization to describe the complex
macromolecule, protein based on the
degree of complexity of of the
molecule. They are Primary
Structure, Secondary structure,
Tertiary structure and Quaternary
structure.
 Primary
Structure of
Protein
Primary structure of protein is the
linear sequence of amino acids that
make up the polypeptide chain.
his sequence is given by the
sequence of nucleotide bases of the
DNA in the genetic code.
The amino acid sequence
determines the positioning of the
different R groups relative to each
other.
 Secondary
Structure of
Protein
The linear, unfolded structure of
polypeptide chain assumes helical
shape to produce the secondary
structure.
The secondary structure refers to the
regular folding pattern of twists and
kinks of the polypeptide chain.
The regular pattern is due to the
hydrogen bond formation between
atoms of the amino acid backbone of
 Tertiary Structure
of Protein
Tertiary structure of proteins is the
three dimensional structure formed
by the bending and twisting of the
polypeptide chain. The linear
sequence of polypeptide chain is
folded into compact globular
structure. The folding of the
polypeptide chain is stabilized by
weak, noncovalent interactions.
These interactions are hydrogen
 Quaternary
Structure of
SomeProtein
proteins contain more than
one polypeptide chains, this
association of polypeptide chains
refers to the quaternary structure.
Each polypeptide chain is called
a subunit.
The subunits can be same or
different ones.
Example: Haemoglobin the oxygen
carrying component of blood is made
 Function of
Proteins
Proteins are seen in muscles, hair,
skin and other tissues, they
constitute the bulk of body's non-
skeletal structure. Example: The
protein keratin is present in nails and
hair.

Some proteins are hormones and

regulate many body functions.
Example: Insulin hormone is a
 Types of Proteins

The types of proteins are as follows:

Hormones are the proteins based
chemicals that are secreted by the
endocrine glands. Hormones are
chemical messengers, that transmit
signals from one cell to the other.
Enzymatic proteins accelerate the
metabolic activity in the cells.
Structural proteins are necessary
components of the body. Structural
 Examples of
Proteins
Examples of fibrous proteins:

Actin, Collagen, Elastin, Fibronectin,

Keratin, Myosin, Tropomyosin,
Tubulin, etc

Examples of globular proteins:

Albumins, Alpha globulin, Beta

globulin, Cadherin, Fibrin, Gamma
 Class 4: Nucleic Acids
Nucleic acids are organic compounds with
heterocyclic rings. Nucleic acids are made of
polymer of nucleotides. Nucleotides consists
of nitrogenous base, a pentose sugar and a
phosphate group. A nucleoside is made of
nitrogenous base attached to a pentose
sugar. The nitrogenous bases are adenine,
guanine, thyamine, cytosine and uracil.
Polymerized nucleotides form
deoxyribonucleic acid (DNA) and ribonucleic
acid (RNA) which are genetic material.
 Nucleic Acids

Nucleic acids are large organic

compounds found in the
chromosomes of living cells and
viruses. They are strong acids found
in the nucleus of the cells. The
nucleic acid polymers are with
high molecular weights as high as
100,000,000 grams per mole. With
proteins, nucleic acids are most
important biological macromolecules.
 History

In 1869, Friedrich Miescher isolated

nuclei from pus cell and found that
they contained phosphate-rich
substance, he named it nuclein.

In 1899, Altmann, introduced the

term nuclei acid. Fischer in the
Nucleic Acid Definition
Back to Top

Nucleic acids are essential large

biological molecules for all forms of
life. The nucleic acids include the
DNA and the RNA. They are the
hereditary determinants of living
organisms. They are present in most
living cells either in free state or
 Properties of
Nucleic Acids
Properties of nucleic acids are as
follows:
Nucleic acids (DNA and RNA) are
long polymers made of repeating
units of nucleotides.

Nucleotide units are made of

phosphate-sugar-nitrogenous base
units.
Types of Nucleic
Acids

Nucleic acids are

of two types DNA
and RNA
 DNA
(deoxyribonucleic
acid)
DNA is one of the macromolecules,
they are essential to all living forms.
Deoxyribonucleic acid contains
the genetic information, it is used in
the development and functioning of
all living organisms.
The DNA segments carry genetic
information are called the genes.
Other DNA segments have structural
functions or regulate the genetic
 RNA (ribonucleic
acid)
The functions of ribonucleic acid is to
convert genetic information from
genes into amino acid sequences of
protein.
In some viruses, RNA contains the
genetic information.
RNA is of three types, they are tRNA
(transfer RNA), mRNA (messenger
RNA) and rRNA (ribosomal RNA).
Messenger RNA, as the name
 Structure of
Nucleic Acids
Structure of nucleic acids DNA and
RNA are similar. The structure is
divided into four different levels,
primary, secondary, tertiary and
quaternary.
Primary structure of nucleic acids is
a linear sequence of nucleotides,
which are linked to each other by
phosphodiester
linkages. Nucleotides are made up of
three components - Nitrogenous
base, 5-carbon sugar and phosphate
groups.
Nitrogenous base are
purines(adenine, guanine) and
 Secondary
Structure
Secondary structure is the interaction
between the bases. This structure
shows parts of which strands are
bound to each other. The two strands
of DNA in the double helix of the
DNA are bound to each other by
hydrogen bounds. The nucleotides
on one strand base pairs with the
nucleotides of the other strand. The
secondary structure of the DNA is
Tertiary structure is the three
dimensional shape into which the
entire chain is folded. Tertiary
structure arrangement differs in four
structural forms:
Left or right handedness.
Length of the turn of the helix.
Number of base pairs per turn.
The difference in size between major
and the minor groove.
 Quaternary
Structure
Quaternary structure is the higher-
level of organization of the nucleic
acids. This structure refers to the
interactions of the nucleic acids with
the other molecules. The most
commonly seen organization is the
form of chromatin which shows
interaction with small proteins
histones.
 Functions of
Nucleic Acids
The main functions is store and
transfer genetic information.

To use the genetic information to

direct the synthesis of new protein.

The deoxyribonucleic acid is the

storage for place for genetic
information in the cell.