C H A P T E R

1
Earth
Biosphere
Biome
Ecosystem
Community
Population
Organism
Systems
Organs
Tissues
Cells
Organelles
Molecules
Atoms
The chemical
nature of
the cell
The chemical
nature of
the cell
The chemical
nature of
the cell
3
Chapter 1 The chemical
nature of the cell
Key knowledge
The chemical nature of the cell
synthesis of macromolecules: polysaccharides, nucleic acids and proteins
the structure and function of lipids
the structure and function of DNA and RNA
the structure and functional diversity of proteins: the proteome
We are one of 1.4 million different life forms that have so far been identied on
Earth. This seems a large number but it probably represents only a third of all the
species that exist on our planet. Although the possibility of life forms beyond our
planet intrigues us, those on Earth share characteristics that dene them as living.
Whether a bacterium, whale, fungus, tomato plant or snail, living things have
certain characteristics in common: movement, growth and the ability to replicate
or reproduce themselves. They detect and respond to changes in their environment,
they take in food or matter, and process it in a variety of ways that involve controlled
transformation of energy, and they remove the waste products of their activities.
All parts of living things are made by the activity of their cells: the slime on the
back of a frog, the extraordinary exoskeletons that many insects have, the bark of
trees, the skin of grapes and the ngernails of your hand. All living things produce
substances that help them live. For example, bees produce the wax that forms their
honeycombs, spiders produce the silk of their webs to trap their prey, and the squid
and the skink both produce ink that they squirt to confound their attackers.
Over the past 150 years we have come to understand that all organisms are made
up of structural units, cells, which can be found in many shapes and sizes depending
on where they are located in the organism and the job that they have to do. These
cells arise from pre-existing cells. Some organisms consist of single cells, while
others consist of millions upon millions of cells organised into functional groupings
according to what they contribute to the organism as a whole: the leaf and roots of a
plant, the muscles that make wings ap, the gills of a sh, the heart that pumps blood
and the contractile tissues of a jellysh that propel it on its way.
Before we knew about cells and the biochemical processes that they carry out,
it was thought that maggots, moulds and eas could spontaneously generate from
inanimate objects, such as old paper, dirty clothing and leftover food.
The chemical basis of life
Through a long history of experimentation and observation using increasingly
sophisticated technologies we have come to know much more about what cells are
composed of. We now have a better understanding of how their composition relates
to what they do, and what they need to be able to do it.
Figure 1.1 The variety of life forms
on Earth can look very different but
they all have a common structural and
chemical organisation. (a) Bacteria,
such as this Helicobacter pylori are
single-celled organisms. Multicellular
organisms are represented by a
diversity of forms, such as this
(b) humpback whale and (c) banksia
a
b
c
4 Unit 3
Each cell is a highly organised assembly of atoms and molecules, which interact
in thousands of simultaneous chemical reactions. For example, most animals die in a
few days without water and in a few minutes without oxygen. Some bacteria die in the
presence of oxygen! Without a daily intake of magnesium, body muscles become sore
and weak and the human brain fails to work properly, and plants turn yellow and die.
Such observations conrm that organisms are composed of chemicals that react with
each other and with many substances in the environment.
Our knowledge of the molecules that make up the cell and the biochemical
activities that they are involved in has led to our ability to apply this knowledge,
seemingly to our benet, in, for example, medical diagnosis, designer pharmaceuticals
and vaccines. New, exciting elds of bioscience are expanding, such as genomics and
proteomics. These deal with our understanding of deoxyribonucleic acid (DNA)
our genetic material and how it can be manipulated to change the very nature of
life itself. The universality of DNA denes life as we know it its presence in all
known living things is an indicator of life.
New ways of storing and analysing data known as bioinformatics have evolved to
generate and deal with the vast amount of information that is associated with research
into molecular biology.
The cell a chemical factory
Each cell can be viewed as a chemical factory, which is programmed by information
stored within the organisms genetic material, the DNA molecule. Like any factory,
the cell has inputs the variety of raw materials that are processed by specialised
enzymes or protein machines and outputs the products of such activities.
Some of the products are used within the cell, whereas others are packaged and
exported for use elsewhere.
A cell, like any efcient factory, requires a supply of energy to maintain
production. It needs an effective means of communication to coordinate internal
cellular activities and those that take place in other parts of the organism.
Trying to understand the nature of the cell without some knowledge of chemistry
would be like trying to read a book without any knowledge of the language it
is written in! The focus of this chapter is on the major groups of biomolecules
which cells, and therefore living things, are made from proteins, nucleic acids,
carbohydrates and lipids what they are, how they are synthesised, and the part that
they play in the structure and function of the cell.
These biomolecules are indeed the signatures of life. But, rst, let us review some
chemical signposts that will help us navigate the journey into the molecular world of
the cell.
The nature of matter
The living world has an important feature in common with the non-living world
matter. All substances, whether solid, liquid or gas or even something in between such
as plasma, are composed of matter. Matter has mass and takes up space; it consists of
particles called atoms. An atom has a nucleus containing positively charged protons
and neutrons, which have no charge. Negatively charged electrons spin around the
bioTERMS
genomics
the study of the genome how
genes interact with each other
and the environment and the
resultant proteins produced;
it requires a knowledge of an
organisms entire DNA sequence
so studies rely on powerful
computer technologies
proteomics
the study of the structure and
function of proteins, including
the way they work and interact
with each other inside cells
bioinformatics
the science of managing and
analysing biological data using
advanced computing techniques;
it is especially important in
genomics research because of
the large amount of complex data
this research generates
biomolecules
molecules that have important
structural or functional roles in
cells
B
I
O
L
I
N
K
Cell revision
5
Chapter 1 The chemical
nature of the cell
nucleus in regions of space known as orbitals (Figure 1.2). A neutral atom has no net
charge as the number of electrons is equal to the number of protons in the nucleus.
Information about atoms and their subatomic particles is written in a standard
chemical notation. This is shown in Figure 1.3.
The elements of life
Atoms are the building blocks of substances. Each kind of atom has its own
distinctive set of characteristics. A substance consisting entirely of one type of atom
is an element. For example, the element carbon is composed of atoms that all contain
6 protons in the nucleus; nitrogen, a colourless gas, has 7 protons in its nucleus. The
number of protons within a nucleus denes the element.
Is carbon the key?
Interestingly, all the chemicals of life on this planet, with the exception of water, are
based on the carbon atom. Compounds that contain carbon atoms, with a few notable
exceptions such as carbon dioxide, are called organic compounds and the study of
them is termed organic chemistry.
Less than 200 years ago, scientists thought that organic compounds could only be
produced in living things. In 1828, the German chemist Wohler showed that urea, a
nitrogenous compound found in urine, could be made by heating ammonium cyanate
in a test tube. The ability to produce an organic compound outside a living cell put an
end to the notion that some mysterious vital force was required for the production of
compounds in living things.
Other essentials
Nitrogen, a colourless and rather inactive gas that makes up 78% of the Earths
atmosphere, has one more proton in its nucleus than carbon. Nitrogen is signicant to
living things as it is an essential element in proteins.
Carbon (C) and nitrogen (N), together with oxygen (O) and hydrogen (H), make
up 99% of the elements that constitute living things. The remaining 1% contains
many other elements, such as sulfur (S) and phosphorus (P), as well as many metallic
atoms, such as magnesium (Mg), sodium (Na), potassium (K), calcium (Ca) and
iron (Fe).
Some atoms radiate
Some atoms of an element can have more neutrons in their nucleus than others;
they have the same atomic number but their mass number is different. Such atoms are
called isotopes of the element (Figure 1.4). For many elements the extra neutrons in
the nucleus make the atom unstable. To become stable the nucleus breaks apart and
gives off energy, which we call radiation, and the extra neutrons. When this happens
we say that the element decays.
These atoms are radioisotopes of that element and their decay or loss of
subatomic particles is described as radioactivity. By giving off radiation, atoms reach
a more stable state. Radioactive isotopes are useful tools in the study of many areas of
science, including biochemical reactions and medical research (Biobox 1.1) because
their presence can be detected by the radiation they release.
Figure 1.2 The structure of an atom.
The nucleus, which contains positively
charged protons and neutral neutrons,
is surrounded by a cloud of orbiting
negatively charged electrons.
Figure 1.3 Symbolic representation of
an individual atom of an element.
Figure 1.4 Isotopes of carbon.
element

mass number, number of
protons and neutrons
atomic number,
number of protons
X

A
Z
proton neutron
(
12
C) (
14
C)
Carbon-12 Carbon-14
6 protons 6 protons
6 neutrons 8 neutrons
electron
neutron
proton
6 Unit 3
The Chernobyl nuclear reactor disaster occurred
in 1986. It is believed that 5000 people died as a
result of this disaster and the environment will
take generations to recover. The harm of radiation
exposure to living organisms is well documented
but perhaps less is heard of the healing capacity
and research power of radioactive isotopes or
radioisotopes.
Radioactive elements, tracers, are used in
molecular research to investigate the movement of
atoms and molecules through a biological system.
Small amounts of radioactive material are easily
detected and traced.
Some scientists use light and electron
microscopy to locate radioisotopes in a specimen
by autoradiography. Living cells that are exposed
for a small time to a radioactively labelled
compound incorporate the compound, which
then begins to move through cell pathways.
At various intervals the movement of
the radioactive atoms can be traced using
photographic lm. Darkening of the lm occurs
wherever there is radioactivity. Radiographers
wear badges containing lm to monitor their
level of exposure to radiation.
When you watch hospital dramas, such as ER, on television you hear doctors ordering PET (positron
emission tomography) scans to help in diagnosis or they may discuss the levels of radiation therapy for the
treatment of cancer patients. These methods employ radioisotopes in the eld of nuclear medicine.
Doctors are able to detect tumours, aneurysms (weak areas in the walls of blood vessels) and
disorders of organs such as the thyroid gland. Cancer cells can be targeted and killed using radiotherapy.
The level of radiation is closely monitored to target the tumour and limit the damage to healthy cells.
The Chernobyl disaster involved a radioisotope that takes a long time to decay. This is why it created
problems for generations to come. If you were choosing a radioisotope to use in medical diagnosis,
would you choose one with a slow or fast rate of decay?
A farmer was offered three types of fertiliser to use on his crop. Explain how isotope labels such as
nitrogen-15 and phosphorus-32 could be used to determine the optimum fertiliser for his crop.
Radioisotopes are used to treat cancerous growths. How would they exert their effect on a
tumour?
BIOBOX 1.1
THE USE OF RADIOACTIVE ISOTOPES IN BIOMEDICAL
RESEARCH
Figure 1.5 Radiographers prepare a patient for radiotherapy as treatment for a tumour of
the pituitary gland.
7
Chapter 1 The chemical
nature of the cell
Na
+
Cl

Na(2,8,1)
Key
Cl

ion Na
+
ion water molecule H atom O atom
The charged ions are
being pulled away from
the solid salt lattice by
water molecules
Cl (2,8,7)
+
electrolyte
particles
Re vi e w
1 What do living and non-living things have in common?
2 What distinguishes living things from non-living things?
3 If a neutral atom had 6 protons, how many electrons would it have?
4 What subatomic particle denes a particular element?
5 Write the standard notation for the phosphorus atom (P) that
contains 17 neutrons and 15 electrons.
6 Which subatomic particle varies in number in all the isotopes of a
particular element?
7 List the four major elements found in living things.
8 Describe two ways that radioactive isotopes are used in biomedical
research.
Figure 1.6 The ability of an atom to
react with other atoms is determined
by its number of valence, or outer
shell, electrons. When the outer shell
is full, the element is stable and will
not react. Shell 1 is stable with two
electrons, while all other shells are
stable with eight electrons.
Figure 1.7 (a) Sodium metal
and chlorine gas combine to
form table salt, a solid lattice.
(b) Sodium donates a single electron
to chlorine, forming charged ions.
(c) When table salt dissolves in water,
electrolyte particles are liberated.
Atomic
number
Element Number of electrons in shells
Shell 1 Shell 2 Shell 3
1 Hydrogen 1
2 Helium 2
3 Lithium 2 1
6 Carbon 2 4
7 Nitrogen 2 5
8 Oxygen 2 6
10 Neon 2 8
11 Sodium 2 8 1
12 Magnesium 2 8 2
15 Phosphorus 2 8 5
16 Sulfur 2 8 6
17 Chlorine 2 8 7
18 Argon 2 8 8
Does getting together mean staying together?
The number and arrangement of electrons in an atoms outer shell determine
its chemical behaviour or reactivity. Outer shell electrons are called valence
electrons (Figure 1.6). Atoms accept, give away or share their valence electrons
with other atoms, thereby achieving chemical stability.
When atoms of different chemicals combine, compounds form.
These are stable combinations of atoms of different elements that are
held together by chemical bonds. Chemical bonds are forces of attraction
between atoms, and the nature of the bonds differs according to the type of
atoms involved.
Opposites attract
Atoms can lose or gain electrons. Atoms that lose electrons become
positively charged they become positive ions (cations). Metal atoms
tend to form cations. Atoms that gain electrons become negatively charged
they become negative ions (anions). Non-metal atoms tend to form
anions. In general, atoms of metals combine with atoms of non-metals by
transferring their valence electrons. The bond is called an ionic bond. The
resulting compounds are called ionic compounds or salts.
Atoms of metals + atoms of non-metals ionic compounds
(cations) (anions) (solid lattice)
The ionic compound, sodium chloride, is one of the salts found in solution in the
tissue uid that bathes the cells of living organisms. It is formed when sodium and
chlorine, two highly reactive and toxic elements, transfer electrons (Figure 1.7). Salts
are ionic compounds that
dissolve in water as the
bonds holding the ions
together weaken and break,
releasing them. These
particles in solution are
called electrolytes.
outer shell is not full: element will react
full outer shell: the element is unreactive
a
b
c

8 Unit 3
H
O
H
In plants, the transport system carries mineral ions (electrolytes) in solution from
where they are absorbed to where they are required.
Generally, we obtain all the electrolytes we need from our diet. At times we can
suffer dehydration due to excessive diarrhoea, vomiting or strenuous exercise for long
periods. Have you licked your lips and tasted salt? Under these conditions you will
need to replenish the electrolytes and water you have lost. Many sports drinks contain
electrolytes together with carbohydrates for energy, but unless you are an endurance
athlete, it is not necessary to replenish electrolytes in this fashion.
Molecular compounds
A knowledge of how compounds are formed and the
nature of the bonds that hold their atoms together
helps us to understand what goes on in living things.
Sharing is a bonding relationship
Instead of losing or gaining electrons, atoms of
non-metals combine with other non-metal atoms
by sharing pairs of valence electrons, thus forming
molecular compounds. The bonds holding the atoms
in these molecules together are covalent bonds.
Atoms of non-metals + atoms of non-metals molecular compounds
Intramolecular attraction
Most of the molecules that make up cells and control cellular functions are composed
largely of non-metal atoms, such as those of carbon, hydrogen, oxygen and nitrogen.
Proteins and nucleic acids are very large molecules that are made up of many atoms.
To interact and work together, it is important that these particular molecules do not
fall apart easily especially in water, in which most chemical activities take place.
Fortunately, covalent bonds tend to be stronger than ionic bonds but this means that,
to break these bonds, help is needed in the form of special proteins called enzymes.
Covalent bonds in molecules are referred to as intramolecular bonds (intra within).
Intermolecular attraction
Molecules themselves can attract each other. The bonds formed in this way are
referred to as intermolecular bonds (inter between) and result from the polarity
of the molecules. Polarity which can be positive or negative is determined by the
overall shape of the molecule and the distribution of the electron pairs within the
covalent bonds that hold the atoms of the molecule together.
Non-metal atoms do not always share electron pairs with equal pull when they
form covalent bonds. A molecule may end up being lopsided in terms of charge,
with an overall negative charge at one end and an overall positive charge at the other.
Whether molecules are polar (unequal charge distribution) or non-polar (equal
charge distribution) affects their interactions in the cell (Figure 1.9).
Figure 1.8 Atoms share pairs of electrons,
forming covalent bonds, to form a stable
molecule. Two covalent bonds hold one
oxygen and two hydrogen atoms to form
a molecule of water.
bioTERMS
electrolyte
a substance that dissociates into
ions in solution
molecular compounds
substances made up of different
non-metallic elements that form
stable associations owing to the
sharing of outer shell electrons
covalent bonds
strong chemical bonds that form
between non-metal atoms by
the sharing of pairs of outer shell
electrons; bonds may be single
(one pair), double (two pairs) or
triple (three pairs)
enzyme
a specic protein catalyst that
acts to increase the rate of a
chemical reaction within the
cell by lowering the amount of
energy required for the reaction
to proceed
polarity
a term that refers to a molecule
having distinct regions of
opposite charge
9
Chapter 1 The chemical
nature of the cell
The nal overall charge on a molecule depends on two factors: the degree of
polarity of the covalent bonds between atoms in the molecule, and the shape of the
molecule itself.
Molecular representations
The world at the atomic or molecular level is not visible yet we need some way of
representing our knowledge of matter. Scientists have developed standard chemical
shorthand and visual representations that convey such information.
Formulae: show the number and kinds of elements that form particular functional
groups and molecules of substances.
Structural formulae and ball-and-stick models: conventional ways of representing
how groups of atoms are arranged and bond.
Space-lling models: advanced computer imaging technologies show three-
dimensionally how molecules occupy space.
Table 1.1 Ways of representing molecules
Substance Chemical
formula
Structural
formula of
subunit
Ball-and-stick
model
Space-lling
model
Methane CH
4
Ammonia NH
3
Water H
2
O
Key C H O N
Figure 1.9 Polar and non-polar
molecules. (a) Two hydrogen atoms
share their electrons equally so the
hydrogen molecule is non-polar.
(b) In hydrogen chloride, the chlorine
atom has a greater pull on the
shared pair of electrons so its end is
comparatively negative. The molecule
is polar.
bioTERMS
non-polar
a molecule that disperses charge
evenly; it lacks a particular
charged end
polar
a molecule with an uneven
distribution of charge giving it
distinct charged ends
Re vi e w
9 What is a compound?
10 Draw up a table that summarises the similarities and differences between molecular and ionic
compounds.
11 How does the formation of molecular compounds differ from ionic compounds?
12 What is a chemical bond?
13 Distinguish between polar and non-polar molecules.
H H
H Cl

a
b
C
H
H
H H
N
H
H
H
O
H
H
10 Unit 3
Water the wonder molecule
Water is one of the most signicant compounds on our planet. Our search on Mars
for water catches the imagination not only of explorers of space. If water is there, does
that mean that life as we know it is, or was, there too? What makes water such an
important indicator of life?
All known life forms require water. It is the most abundant compound in cells
and organisms. About 7585% of a cell by weight is water. Practically all substances
and chemical processes of biological signicance occur in a watery medium; aqueous
solutions constantly bathe cells; water covers nearly 72% of the Earth and is home to
a vast array of living things from the surface to the depths. It inuences the cycling of
matter between the living and the non-living components of ecosystems.
Water molecules are highly polar; the oxygen end of a molecule is negative so it is
attracted to the positive end of a nearby water molecule and forms hydrogen bonds
with it (Figure 1.10).
Hydrogen bonding explains many of the properties of water that are essential for
life.
Chemical properties of water
Dissolve or not?
More substances dissolve in water than in any other liquid. This ability is due to the
polarity of water molecules; it means that water molecules can interact with other
charged particles, such as polar molecules or ions.
Polar molecules can form hydrogen bonds with polar molecules of water and so
dissolve they are called hydrophilic (water loving). However, non-polar substances
will not dissolve in water because they cannot form hydrogen bonds with water
molecules they are hydrophobic.
Polar solvent (e.g. water) + polar solute solution
Oil and petrol are non-polar substances. They do not dissolve in water but they do
dissolve in each other (Biobox 1.2). What kind of substance will you use to remove
the grease on your clothes?
Non-polar solvent + non-polar solute solution
Thus, for substances to form a solution, the rule is that like dissolves like.
Most gases, such as oxygen and carbon dioxide, consist of very small molecules
and dissolve in water because they t between the water molecules in the spaces that
are created by hydrogen bonding.
Concentrate on the solution
The concentration of uids in and around cells affects their functioning. Movement
of water molecules and other substances across the plasma membranes of cells and
their organelles is affected by the relative concentrations of the substances on either
side. Biochemical processes usually take place within a certain range of conditions,
one being the acidity of the solution.
Figure 1.10 Water molecules form
hydrogen bonds with each other.
Each molecule forms hydrogen
bonds with up to four neighbouring
molecules.
bioTERMS
hydrogen bond
a weak intermolecular chemical
bond between a hydrogen atom
on one molecule and a second,
more electronegative element,
usually an oxygen or nitrogen
atom on another molecule;
hydrogen bonds are important
in the specicity of base pairing
in nucleic acids and in the
determination of protein shape
hydrophilic
substances, such as polar
molecules and ionic compounds,
which dissolve readily in water
because they readily form
hydrogen bonds with water
molecules
hydrophobic
substances, such as non-polar
molecules, that are insoluble in
water
Chapter 1 The chemical
nature of the cell
11
If we mix up a salad dressing before we pour it onto a salad, no matter how hard we shake the bottle, the oil and
water always separate when we stop mixing. The oil sits on top and we end up with an oily dressing. Australian
scientist, Professor Ric Pashley, has turned this notion on its head to show that oil and water can mix. His discoveries
have far-reaching implications beyond the less oily salad!
Pashley knew that all liquids contain gases that dissolve into them from the atmosphere. When he pulled a
single oil droplet apart in water he noticed gas bubbling out of the water. This gas was forming a bridge between the
two new oil droplets and pulling them back together. He decided to investigate whether this was the reason that oil
could not disperse in water. He removed the gases from both the oil and water layers by freezing a mixture in liquid
nitrogen. As it thawed he saw gas
bubbling out. After a number of
cycles the sample was gas-free. It
had become cloudy from tiny oil
droplets that dispersed throughout
the solution.
So oil and water can mix.
All that we need to do to a salad
dressing is remove the gas! This is
not an easy task to perform in the
home but food, pharmaceutical
and cosmetics industries are
developing cost-effective ways to
embrace this new technology.
Many of the drugs used
in hospital treatments are oily
and so are difcult to get into
the bloodstream. To date,
detergents or solvents, which
often produce side-effects, are
required to mix the drugs with water. Using Pashleys discovery, drugs will disperse through water in tiny droplets
that are easy for the body to absorb.
Future washing-machine designs will involve technology to remove gas from water rather than for adding
detergent to water. This means that oil-stain removal will require simply to add water. The benets to the
environment would be substantial.
Many cosmetics, especially creams and lotions, contain oily substances, such as essential oils, as well
as water and other ingredients that are not miscible with oils. How do the two mix? Generally, solvents are
utilised, many of which actually dry out the skin. Solvents will be redundant in the cosmetics industry as oils
will disperse in gas-free water.
Describe what generally happens when you stop shaking a mixture of oil and water.
How can you get oil to disperse uniformly through water?
Suggest some ways that industry will utilise this technique of mixing oil uniformly throughout water.
BIOBOX 1.2
OIL AND WATER CAN MIX
Figure 1.11 Can oil and water mix?
12 Unit 3
Gastric
juice
12
Lemon
juice
2.4
Orange
juice
3.5
Soda water
56
Milk
6.5
Pure
water
7
Blood
7.4
Household
ammonia
11
concentration of H
3
O
+
is 10
1
M
neutral
concentration of H
3
O
+
is 10
14
M
1 2 3 4 5 6 7 8 9 10 11 12 13 14
solution increasingly acidic solution increasingly basic
Acids, bases and buffers
An acid is a substance that produces hydrogen ions, H
+
, in solution. The acidity of
a solution is measured by its pH. The lower the pH, the more acidic a solution
(Figure 1.12).
Figure 1.12 A base is a substance that
will take hydrogen ions from an acid.
If sufcient base is added to an acid, it
will neutralise the acid so its pH is the
same as that of pure water. (a) The pH
scale. (b) Typical pH values of some
common solutions.
Many chemical reactions within cells produce acidic or basic substances. However,
it is vital that blood pH is maintained within very narrow limits, with a mean value
of 7.4. A deviation of more than 0.4 would be fatal, as many vital cell reactions could
no longer occur. Such deviations are prevented by buffering systems. These contain a
mixture of a weak acid and the particle that results when it has given away a hydrogen
ion. (This particle is termed its conjugate base, as it can accept a hydrogen ion from
an acid to reform the weak acid.) A buffering system will react with any acid or base
that is added, and maintain a steady pH by either releasing more hydrogen ions or
using up excess hydrogen ions.
One of the major buffering systems in our bloodstream is the carbonic acid-
bicarbonate system (Figure 1.13). Carbonic acid is a weak acid and the bicarbonate
ion is its conjugate base. The reversible arrows show the reactions can go back and
forth, which allows them to respond to any acidic or basic substance that enters our
bloodstream. The other major buffering system involves our haemoglobin.
Physical properties of water
The physical properties of water have a profound effect on living things too. Table 1.2
summarises the properties of water. The difference between the solid and liquid
structures of water make it essential to support life as we know it (Figure 1.14).
Figure 1.13 Carbon dioxide reacts with water in the
blood to form carbonic acid. Carbonic acid dissociates,
releasing bicarbonate ions and protons that react with
acids and bases in the blood. This buffer system keeps
the blood at a relatively constant pH of 7.4.
Figure 1.14 As water cools the water
molecules move further apart reducing
the density, so ice oats on water.
a
b
CO
2
+ H
2
O H
2
C0
3
HCO
3
+ H
+
carbon water carbonic bicarbonate hydrogen
dioxide acid ion ion
_
ice (solid)
water (liquid)
Key
oxygen atom

hydrogen atom

H bonding
13
Chapter 1 The chemical
nature of the cell
b a
Table 1.2 Properties of water
Feature Property Explanation Effect Example
Water molecules
attract each other
Cohesion (see
Figure 1.15)
Water molecules form hydrogen bonds with
each other.
High surface
tension
Some insects can walk on water. The
pulling power of water molecules on each
other assists upward movement of water
in the transpiration stream of plants.
Water molecules
attract other polar
molecules
Adhesion (see
Figure 1.15)
Water molecules form hydrogen bonds with
other polar molecules.
Capillarity Water can creep up narrow spaces.
Capillarity assists the movement of water
and solutes in plant stems and roots.
Absorbs much heat Retains heat
readily
Hydrogen bonds enable water to absorb
relatively large amounts of heat before its
temperature rises, and lose relatively large
amounts of heat before its temperature drops.
Temperature
uctuations
are minimal
Assists thermoregulation; serves as a
heat reservoir in cold climates.
Requires a large
amount of heat
before changing
from liquid to vapour
Specic heat is
high
Hydrogen bonds enable water to absorb
relatively large amounts of heat before
changing from liquid to gas (vapour).
Cooling by
evaporation
is efcient
Crocodiles gape and dogs pant to
increase loss of heat by evaporation.
Many animals sweat (Figure 1.16b).
Liquid water is more
dense than solid
water (ice)
Highest
density of
water is at 4C
As water molecules cool below 0C they form a
crystalline lattice. The hydrogen bonds spread
the molecules apart, thus taking up more
space and reducing the density of the water
(solid) (Figure 1.14).
Ice oats on
liquid water
Aquatic organisms are able to survive
below ice in cold conditions (Figure
1.16a).
Figure 1.16 Water and its signicance
to life. (a) Water freezes from the top
down and ice oats on water, allowing
sea and pond life to exist in freezing
climates. (b) The properties of water
allow us to cool down when we sweat.
cohesion
water molecules adhere
to cellulose in xylem
vessel wall
oxygen
hydrogen
hydrogen bond
Figure 1.15 Intermolecular bonds.
Hydrogen bonds between water
molecules make them cohere. Water
molecules can adhere to surfaces that
consist of polar molecules.
14 Unit 3
lipid
(e.g. triacylglycerol)

Biomolecules
carbohydrate
(e.g. starch)
nucleic acid
(e.g. DNA)
protein
(e.g. enzyme)
The big ones biological
macromolecules
Every living cell is involved in synthesising large molecules that are needed not only
to build the body parts of organisms but also to maintain the biochemical processes
that keep them living: communication, transforming energy and relaying genetic
information.
These large molecules are called macromolecules (macro big) and are grouped
into four main classes based on their chemical composition and structure. The four
classes are proteins, nucleic acids, complex carbohydrates and lipids. Each of these
groups is further subdivided according to their slight differences in structure and,
therefore, in function.
Re vi e w
14 Explain the attraction of water molecules
to one another and its signicance.
15 Explain why a hydrophilic substance,
such as alcohol, readily dissolves in water.
16 What property of water accounts for each
of the following observations?
a Dogs pant on a hot day.
b Water creeps up the walls of a glass
tube.
17 What is pH? How do buffers adjust the
pH level of cells?
18 Why does solid water oat on liquid
water? Of what signicance is this to
living things?
As we shall see, each kind of biomacromolecule has characteristics or
properties that make it effective for carrying out its particular function: the
structure and properties suit the purpose. Each kind of biomacromolecule
consists of smaller components, as shown in Table 1.3.
Table 1.3 Major macromolecules
and their subunits
Macromolecule Subunits
Complex carbohydrate Simple sugar
(monosaccharide)
Lipid Triglyceride and
chains of fatty acids
Protein Amino acid
Nucleic acid (DNA, RNA) Nucleotide
bioTERMS
lipids
a general term for fats, oils and
waxes; they are insoluble in
water and largely made up of
molecules containing carbon,
hydrogen, oxygen and, at times,
phosphorus and nitrogen
nucleic acids
large polymers made up of
nucleotides; deoxyribonucleic
acid and ribonucleic acid are
the information-carrying
molecules of the cell and carry
the instructions for making all
the structures and materials the
body needs to function
protein
a polymeric macromolecule built
up of amino acid monomers;
proteins have specic structural
and functional roles in living
things and are produced from
the information encoded in an
organisms genetic material
Figure 1.17 The major groups
of biological macromolecules.
Chapter 1 The chemical
nature of the cell
15
Throughout 2004 two amazing machines have been tracking their way across the surface of the planet
Mars. Part of their mission is to search for molecules that could have originated from life as we know
it. The detection of methane gas, a hydrocarbon molecule, in the Martian atmosphere has raised some
interesting questions. On Earth, the production of methane gas is due to the action of various bacteria.
However, volcanic eruptions can also produce the gas. The jury is still out on the origin of the methane
gas detected on Mars.
Hydrocarbon molecules provide the backbone to many important biological molecules and so
their presence can be an indicator of life. As their name suggests, hydrocarbons are molecules that are
made up of only carbon and hydrogen atoms. We may hear of them in relation to petroleum, which is
a complex mixture of different hydrocarbons, but all have their origin in living things.
An important property of hydrocarbons is their insolubility in water they are hydrophobic but
they do dissolve other non-polar molecules so are well known as solvents.
Functional groups
The many chemical properties observed in organic molecules are due to the addition of special
groups of atoms to the hydrocarbon backbone. These groups of atoms, which determine the
characteristics of many biomolecules, are called functional groups. They are more reactive than the
hydrocarbon portion of the molecule and inuence the molecular interactions that occur between
molecules. Many functional groups carry a positive or negative charge, and when attached to a
hydrocarbon make the whole molecule charged this makes the molecule soluble in water.
Table 1.4 The common functional groups found in biological molecules
Group Chemical formula Found in:
Hydroxyl OH Alcohols (e.g. ethanol)
Carboxyl COOH Acids (e.g. vinegar)
Amino NH
2
Bases (e.g. ammonia)
Sulfhydryl SH Rubber
Phosphate PO
4
ATP and DNA
Carbonyl COH
CO
Aldehydes (e.g.
formaldehyde)
Ketones (e.g. acetone)
Coal is a fossil fuel that contains hydrocarbon molecules. What are these hydrocarbon
molecules composed of and where did they come from originally?
Hydrocarbons are non-polar molecules that are insoluble in water. What must be added to
these molecules to make them water-soluble?
Which is the functional group found on all alcohol molecules?
BIOBOX 1.3
HYDROCARBON MOLECULES
16 Unit 3
Synthesis of biomacromolecules
Some organisms are able to synthesise their own biological macromolecules, whereas
others synthesise them from organic compounds that they have ingested. Organisms
that can synthesise their own organic compounds from the inorganic materials that
they take in from their surroundings are called autotrophs (self-feeders). For example,
seaweeds, eucalypts, grass and microscopic algae all produce the basic building
unit simple sugars through the process of photosynthesis. From these products,
autotrophs then synthesise the other kinds of organic compounds that they need.
Some autotrophic organisms, such as certain kinds of bacteria, are able to
synthesise their organic requirements through chemical processes other than
photosynthesis. These organisms are described as chemosynthetic autotrophs or
chemotrophs, and are typically found in extreme conditions, such as in the depths of
the ocean near hydrothermal vents, in thermal springs or in places deprived of oxygen
or light.
Heterotrophs, such as humans are, have to synthesise their own
biomacromolecules from existing organic compounds. Heterotrophs have to take
in a range of organic compounds in their food, which they then break down into
simpler substances. These are then synthesised, or built up, into the kinds of organic
compounds that are required by the organism.
Making a polymer
Large biomacromolecules are synthesised on site inside the cell. Proteins, nucleic acids
and complex carbohydrates are built up by linking smaller repeating molecules, each
called a monomer (mono one, mer unit), to form long chains called polymers
(poly many). This process is known as polymerisation. Even though lipids are large
biomolecules, they are not polymers; they are composed of distinct chemical groups of
atoms.
Monomers link together when the hydroxyl (OH) group of one monomer reacts
with a hydrogen atom of another monomer, forming a water molecule. Thus, the
reaction is called condensation polymerisation.
polymerisation
Single units (monomers) many linked units (polymer)
(subunits) (macromolecules)
Successive monomers are added in the same way to produce a long polymer chain
(see Figure 1.19).
bioTERMS
autotroph
an organism that makes its
own food from light energy or
chemical energy without eating;
most green plants, many protists
(one-celled organisms such as
slime moulds) and most bacteria
are autotrophs
chemotroph
an organism that obtains its
energy from the oxidation of
chemical compounds
heterotrophs
organisms that consume other
organisms as food; organisms
that are not able to make organic
molecules from simple inorganic
compounds
Figure 1.18 Sources of organic
compounds for heterotrophs.
bioBYTE
CSIRO scientists are turning to polymers to replace the metallic pins and screws
currently used by surgeons to heal broken bones. Specially designed gels applied by
injection to the fracture or break form polymers that glue the fractured bone together. This
provides support for the healing process. The polymer will naturally degrade at the same rate
as healing takes place, so no follow-up surgery is required.
The polymers in medicine are non-invasive, recruit body cells to aid healing and are
biodegradable. The possibilities for polymer technology in tissue engineering are vast, with
scientists working on polymers that promote wound care, improvement in drug delivery, and
on polymers that will keep blood vessels open after a blockage has been removed.
17
Chapter 1 The chemical
nature of the cell
Peptide bond
H
2
N
C
C
N
C
C
N
C
C
N
C
C
O R H O R
O H R O H R
N
C
COOH
H
R
Growing Polypeptide chain (polymer) + Amino Acid (monomer)
ATP
ADP
+Pi
H
2
0
H
2
N
C
C
N
C
C
N
C
C
N
C
C
O R H O R
O H R O H R
Amino terminus N
C
COOH
H
R
Carboxy terminus
OH + H
Carbohydrates
Carbohydrates are the most common compounds in living things. We see and hear
about them constantly in relation to our diet.
Their name gives a clue to the composition of carbohydrates. Each molecule
consists of carbon, hydrogen and oxygen atoms in the ratio of 1:2:1, giving the general
formula for carbohydrates of nCH
2
O.
Carbohydrates are classied as monosaccharides, or simple sugars (Figure 1.20a),
disaccharides (Figure 1.20b) and polysaccharides (Figure 1.20c) depending on the
complexity of the linkages of the monomers (Table 1.5).
Organisms use carbohydrates as an energy source and for structural components
(Figure 1.21). Carbohydrate molecules can combine with other atoms or groups to
form important compounds, for example, glycoproteins, which are a combination of
carbohydrate and protein molecules.
Figure 1.19 Polypeptide molecules
form when amino acids are linked
together. These reactions occur
at cell ribosomes that use energy
provided by ATP molecules to form
peptide bonds between amino
acids. Water is generated in these
condensation polymerisation
reactions.
Re vi e w
19 What are the four main types of macromolecules found in all organisms?
20 Which macromolecules are polymers?
21 Describe, by means of an annotated diagram, the process of condensation polymerisation of an example used in the text.
22 Distinguish between autotrophs and heterotrophs in sourcing nutrients to build their macromolecules.
18 Unit 3
O
H
|
C
|
HO
H
|
C
|
OH
H
|
C
|
OH
C
OH
|
C
|
H
glucose
a
O O
|
O
|
H CH
2
OH
glucose fructose
sucrose
b
Figure 1.20 (a) Glucose is a
monosaccharide. (b) Sucrose
is a disaccharide, a glucose and
fructose sugar joined by an alpha
(12) glycosidic bond.
(c) Cellulose is a polysaccharide,
its many glucose units are joined
by beta (14) glycosidic bonds.
Table 1.5 Classes of carbohydrates
Carbohydrate Example Description Location and function
Monosaccharides
(mono = one,
saccharide = sugar)
Triose (e.g.
glyceraldehyde)
Single chain of carbon atoms to which hydroxyl
groups are attached. Soluble in water.
An intermediate compound in carbohydrate
metabolism
Pentose (e.g.
ribose)
Five carbon atoms in backbone; ring structure Sugar unit in RNA molecules
Hexose (e.g.
glucose)
Six carbon atoms in backbone Makes jelly beans sweet; it is an ideal quick energy x
Disaccharides
(di = two)
Maltose Two glucose units linked by an -glycosidic link Found in high concentrations in some grains
Sucrose Glucose and fructose bonded Table sugar, sugar cane, sugar beet
Lactose Glucose and galactose bond together In milk
Polysaccharides
(poly = many)
Complex carbohydrates composed of several
hundred to several thousand monomers in chains
Energy storage and structural support
Cellulose Straight chains that lie next to each other,
promoting hydrogen bonding between them and
producing tight bundles called microbrils.
Form tough, insoluble bres giving structural
support to plant cells. This is the most abundant
organic chemical on Earth.
Starch Mixture of two different polysaccharides linked in
branched and sometimes twisted chains.
Energy storage in plants (e.g. starch grains in seeds
of wheat, corn)
Glycogen Storage compound in animals Energy storage in muscles and liver of animals
Chitin Cellulose-like polymer: each monomer glucose
molecule has an N-containing group attached.
Present in the hard exoskeleton of insects and of
crustaceans, such as crabs; in cell walls of fungi, such
as mushrooms
C
O
O
OH
O
OH
O
O
O
OH
O
OH
O
O
O
OH
O
OH
O
OH
O
O
O
OH
O
OH
O
O
O
OH
O
OH
O
O
OH
chains held together
by hydrogen bonds
cellulose
B
I
O
L
I
N
K
Carbohydrates
19
Chapter 1 The chemical
nature of the cell
Cellulose and the record
Cellulose has the record of being the most abundant organic compound found in
nature. Worldwide, plants are estimated to produce 170 billion tonnes of cellulose
each year. Major industries depend on the brous parts of plants for timber
construction, making paper and manufacturing cloth, such as cotton, hemp and linen
from ax.
Cellulose is an important component of the human diet. It helps to clear out
the digestive system by scraping the lining of the large intestine. This stimulates
the secretion of mucus, which helps solids move their slippery way along the tract.
Constipated? Eat more bre!
But cellulose does not supply us with any nutrients. We lack the enzyme required
to break the bonds that link the glucose monomers in this polymer. Cattle, koalas,
kangaroos and other herbivores host large bacterial populations that can digest
Figure 1.21 Polysaccharides provide
storage, such as (a) starch grains in the
chloroplasts of cells and (b) glycogen
granules in the cytoplasm of animal cells.
They also provide structural support, such
as chitin in (c) the hard exoskeleton of
crustaceans and (d) the cell walls of fungi.
bioBYTE
The Queensland sugar industry is receiving
a new lease of life through the application of
biotechnology. New research aims to improve the
yield of sugar cane products for the manufacture
of bioproducts, such as biodegradable plastic bags
and biofuel, an alternative energy source.
The energy content of biofuels comes from sugars
produced in the process of photosynthesis. Sugar
cane is one of the most effective sugar-producing
organisms on Earth. Sugars produce ethanol, a
fuel that can provide electricity, heat and power
for transport. Ethanol can reduce the use of
conventional non-renewable sources, such as the
environmentally hazardous process of burning fossil
fuels. Fossil fuel is the prime energy source still
used in Victoria.
a
b
c
d
chloroplast
starch
glycogen
granules mitochondrion
20 Unit 3
cellulose. Some herbivores, such as the common ringtail possum (Figure
1.23) and the hamster, actually recycle their cellulose they eat their
cellulose-packed faeces and run them through the digestive system again to
extract the most benet!
Termites have an incredibly important role to play in cycling matter
between the living and non-living components of some ecosystems. The
worker termite caste is able to digest cellulose, which it does through a
symbiotic relationship with unicellular microorganisms in the gut. The
protozoa have enzymes that break down the bonds that hold the monomers
together, liberating the sugar molecules. Termites eat grass, herbs, plant
litter and wood in differing proportions. But in the wrong place at the right
time they wreak havoc on residential and commercial buildings and are
highly destructive timber pests that can cause major structural damage.
All herbivores that eat leaves and wood as the major component of their
diet obtain energy from cellulose. Protozoa and bacteria in their gut do the
work of digesting the cellulose for them. The microorganisms obtain what
they need and the animal benets too. Such relationships are described
as symbiotic and, without them, many forms of life on Earth would
disappear.
Make way for roo-poo paper! Inspiration for making this handmade paper came from Africa, where there is a huge
paper industry based on elephant dung.
A very high percentage of handmade paper is made from cotton
recycled clothes and unused or waste textiles. The rest is made
from plants such as ax, hemp, leaves and stringy bark. What they
have in common is that they are all made of cellulose bres.
The appearance of the roo-poo paper depends on what the kangaroo
has eaten. The dark version looks a bit pooey but without the smell
and the light version has a little cotton added. The kangaroo helps with
the pulping process, as much of it has already been partly digested by
the kangaroos.
The length of bre is signicant: long bres (more than 2 mm)
make stronger paper. Well-chewed plant matter tends to cut the bres
short, so follow elderly roos with worn teeth!
What component of roo poo is utilised for the
manufacture of paper?
What properties of cellulose bres make them
useful for producing paper?
BIOBOX 1.4
ROO POO AND PAPER
Figure 1.23 The ringtail possum can digest the cellulose found in plant matter. To gain maximum
energy from its diet, it digests cellulose a second time by eating its own faeces. Twice the benet!
Figure 1.22 Kangaroos help
in the paper-pulping process
by digesting cellulose.
21
Chapter 1 The chemical
nature of the cell
The average person stores enough glycogen
to last about 12 hours, or 2 hours if exercising
vigorously. Carbohydrate-loading is a legal
method of boosting the amount of glycogen
in the blood prior to a competition. This is
especially important for marathon runners,
who require sustained release of glucose
from the breakdown of glycogen over several
hours.
The process begins six days prior to
an event. In the rst three days the athlete
consumes little to no carbohydrate and
exercises to deplete the bodys glycogen
stores. This tricks the body into starvation
mode as it detects that its glycogen stores
are extremely low. In the last three days
the training load eases off and the athlete
consumes primarily carbohydrate. Still in
starvation mode the body responds by
storing excessive amounts of the newly
available carbohydrate.
What are the monomers that make up the polymer glycogen? Why are they important
to athletes?
Many people who put themselves on strict diets will skip meals or fast in the belief that
this will help them lose weight. What message are they really sending to their body
and what will happen the next time they eat something?
BIOBOX 1.5
GETTING THE BEST FROM CARBOHYDRATES
Figure 1.24 Athletes can improve
their performance by carbohydrate
loading.
Re vi e w
23 Describe the composition of a carbohydrate.
24 What distinguishes the three classes of carbohydrates from each other? Explain how the different classes
of carbohydrates are related to their function.
25 Glycogen and starch are called storage polysaccharides. In what organisms would you nd:
a glycogen?
b starch?
26 Explain why humans obtain limited energy from eating lettuce.
27 Devise a simple diagram that compares the structural polysaccharides that make up the cell walls in plants
and fungi.
22 Unit 3
P
R
A
C
T
I
C
A
L
A
C
TIVIT
Y
1
.1
bioTERM
amphipathic
a molecule in which there is a
difference in water solubility
between one end and the other
owing to differences in polarity
Lipids
Lipids are a diverse group of molecules and include fats and oils, terpenes, waxes,
phospholipids, glycolipids and steroids whose various functions relate to their
hydrophobic nature. In cells, lipids have three important functions:
1 energy storage they have twice the amount of energy as carbohydrates
2 structural component of membranes
3 specic biological functions, such as the transmission of chemical signals both
within and between cells.
Cells also excrete lipids that function to protect the cell or the organism to which
it belongs.
Many plants, such as canola and sunowers, are rich in oils that are harvested
for our use. Oil seeds store energy and matter for growth of new plants. Animals,
such as polar bears, store fat deposits under their skin to get through hard times. Fat
deposits around your vital organs, such as the heart and kidneys, offer protection,
although there can be too much of a good thing.
Whales and seals have great deposits of fat droplets in their adipose
tissue under their skin, which insulates them from heat loss. This
fact has changed the course of history. Whalers and sealers were
famed for their exploits in their search for these magnicent
animals. The oil was more important than the meat. It drove
technology and inuenced culture. It lit the lamps of the 19th
century, extending the hours of light by which people could see,
until replaced by kerosene from petroleum.
Terpenes are a group of lipids that are found as the constituents
of essential oils and they give plants characteristic avours and odours.
Lavender plants produce terpenes that attract insects, whereas citrus
fruits produce terpenes that keep insects away.
Waxes and cutins form protective waterproof coatings in many
organisms. Cutin coats some fruits and bees use beeswax to build their
honeycombs. Many leaves have a cutin coating to stop water from getting out and
diseases from getting in! The renowned Driza-Bone and Japara oilskin jackets owe
their waterproong to the application of waxy substances to their cotton fabric. This
makes water bead and run off.
Whats in a name?
We classify lipids according to their solubility, which depends on the shape of their
molecules and the nature of the intramolecular bonding. Lipid molecules have large
non-polar regions so are hydrophobic and insoluble in water. They do dissolve in other
non-polar substances, such as petrol, according to the like dissolves like rule.
Molecules of some lipids possess a polar end, making the whole molecule partially
polar. These molecules are hydrophilic as they are attracted to the polar water
molecules. Other lipids consist of molecules that have a hydrophobic region and a
hydrophilic region. These are termed amphipathic (amphi both). As we will see
in Chapter 2 this characteristic has an important implication for the structure of
membranes.
F
ig
u
r
e
1
.2
5
The bearded seal gets
p
ro
te
ctio
n
against the cold Arctic waters
fro
m
lip
id
s stored under its skin.
B
I
O
L
I
N
K
Lipids
Chapter 1 The chemical
nature of the cell
The good
Scientists are researching the use of liposomes to deliver drugs to targeted cells. Liposomes are hollow spheres
or micelles that form spontaneously when phospholipids mix in solution. They are able to wrap around or
encapsulate water-soluble drugs in their centres and oil-soluble drugs in their membrane.
Research groups are hoping to use liposomes to deliver genes through the membranes of cells in gene therapy
for patients such as those with cystic brosis.
Scientists are designing liposomes that can evade the immune system, thus giving them time to reach their
target zone.
The bad
Heart disease is among the top causes of death in Western
countries such as Australia. The major cause of heart
disease is atherosclerosis. This disease results from a
narrowing of the arteries, which is caused by a build-up
of cholesterol-rich plaques on their inner lining.
What causes plaques to form? High levels of cholesterol
and triglycerides build up in the blood as a result of
eating too much saturated fat or a defect in the protein,
apolipoprotein E. This protein normally carries cholesterol
molecules to receptors on the surface of liver cells for
removal but, if defective, they cannot and plaques block
the arteries.
Blocked arteries to the heart result in a heart attack
and blocked arteries to the brain result in a stroke a good
diet and exercise help prevent plaque formation.
The ugly
Anabolic steroids are synthetic steroids that are related to the male sex hormones (androgens). They were
developed to promote the growth of skeletal muscle in patients with delayed puberty or wasting of the body
as a result of disease.
Their use is illegal without prescription but some people abuse them to improve athletic ability or body
image. Overuse of anabolic steroids disrupts the normal production of hormones in the body. Particularly,
they cause the level of lipoproteins in the blood to rise, increasing the risk of atherosclerosis and therefore of
stroke or heart attack.
Anabolic steroids resemble the hormone testosterone. In males, they induce body changes such as
the development of breasts and shrinking of the genitals and women show the development of more
masculine features. Both sexes experience loss of head hair and an increase in acne. Their behaviour is
affected too and psychiatric effects can include homicidal rage, mania and delusions.
What property of lipids is employed to create liposomes?
What is atherosclerosis and what are the two main contributors to this disease?
Describe how anabolic steroids work and list the major effects that they have on the human body.
Why were anabolic steroids originally developed?
BIOBOX 1.6
LIPIDS AND YOUR HEALTH
Figure 1.26 Atherosclerosis is a disease caused by cholesterol-rich
plaques blocking arteries, thus reducing the ow of blood.
wall of artery
plaque
23
24 Unit 3
Triglycerides
The fats and oils of plants and animals are typically composed of triglyceride
molecules (Figure 1.27). Their name gives a clue to their composition (tri three)
for the number of fatty acid chains attached to a glycerol backbone.
The structure of the fatty acids attached to the glycerol backbone affects the state
of fats and oils at room temperature. Fats found in animals are solid because their
fatty acids are saturated, making them fairly straight so that they can pack closely
together to form a solid. Oils from plant sources have fatty acids that are unsaturated
they contain double bonds that form bends or kinks so the molecules cannot pack
closely together, giving oils their characteristic liquid form (Table 1.6).
Table 1.6 Differences between saturated and unsaturated fatty acids
Fatty acid Structure Examples
Saturated
(Figure 1.28a)
Single bonds between carbon atoms.
Maximum number of hydrogen atoms attached
to each carbon atom.
Animals: lard, butter, suet, fats,
blubber
Unsaturated
(Figure 1.28b)
Double bonds between some carbon atoms.
Do not have the maximum number of hydrogen
atoms with carbon atoms.
Plants: oils of olives, canola,
sunower, aromatic oils of plants
Lipids in the membranes of cells
Phospholipids form when a phosphate group is added to the glycerol backbone rather
than a third fatty acid chain. The phosphate region is hydrophilic, whereas the fatty
acid tails are hydrophobic so these molecules spontaneously form the lipid bilayers
that make up cell membranes.
Glycolipids form when a carbohydrate group attaches to the glycerol backbone
rather than a third fatty acid chain. They are vital for communication as they are
found projecting from the plasma membrane of cells and are specialised to detect and
bind with signalling molecules.
Cholesterol is a common component of cell membranes (except the inner
membrane of mitochondria and chloroplasts) and of myelin sheaths around nerve
cells. It belongs to the group of lipids collectively
known as steroids. It is important for maintaining a
level of rigidity in cell membranes.
It is also the starting point for the synthesis of all the
steroid hormones, which include bile salts, vitamin D
and the male and female sex hormones, testosterone
and oestrogen (Figure 1.29).
Figure 1.28 Saturated and
unsaturated triglycerides. (a) Butter is
made from animal fat, which consists
of saturated fatty acids. (b) Vegetable
oils are composed of unsaturated fatty
acids, such as oleic acid.
bioBYTE
Current methods of testing for levels of
cholesterol in relation to cardiovascular risk are
costly and take time. Scientists have developed a test
that measures the amount of cholesterol in the skin with
a high degree of accuracy. Early stages of cardiovascular
disease can be detected in seemingly healthy people. In
addition to being very cheap, the test can be used on
patients during routine consultations.
Figure 1.27 (above)
Triacylglycerol is a lipid molecule
that contains a glycerol (alcohol)
unit and three fatty acid chains.
H
|
H C fatty acid chain
|
H C fatty acid chain
|
H C fatty acid chain
|
H
a
stearic acid (saturated)
b
oleic acid (unsaturated)
CH
3
HO
CH
3
CH
3
CH
CH
2
CH
2
CH
2
CH
2
CH
CH
3
CH
3
a
HO
CH
3
OH
b
O
CH
3
OH
CH
3
c
Figure 1.29
The structures of steroids (a) cholesterol,
(b) oestrogen and (c) testosterone
show marked similarities.
bioBYTE
Linus Pauling received the Nobel
Prize for Chemistry in 1954 for his work
on molecular structure and chemical bonds.
Together with Robert Corey, he discovered
the -helix structure in proteins using X-ray
crystallography.
These and studies by others laid the
groundwork for experiments and theory which
eventually led to the discovery of the structure of
DNA in 1953. Pauling was a respected scientist
and social activist. In 1962, he received the
Nobel Peace Prize for his efforts to prevent
the testing and use of nuclear weapons.
25
Chapter 1 The chemical
nature of the cell
Proteins the work horses of the cell
Virtually everything a cell is or does depends on the proteins it contains. What does
your hair have in common with the feathers of birds, the rattle of a rattlesnake and
the spines of an echidna? They are all composed of a strong brous protein known as
keratin. Keratin is just one of an amazing variety of proteins produced by the activities
of cells.
The whole set of proteins produced by a cell is called its
proteome and the study of proteomes is proteomics
a term rst used in 1994 by Marc Wilkins of Macquarie
University, Sydney. Functional proteomics refers
particularly to what proteins do in different cells and
tissues.
Many aspects of protein structure were rst identied
by the father of structural biology, Linus Pauling (1901
94). Since then many scientists have followed in his
footsteps, including world-renowned Australians Sir Gus
Nossal and Peter Doherty, in unravelling the structure
and function of a whole range of different kinds of
proteins in the elds of immunology and microbiology.
Proteins consist of large complex molecules and
are, perhaps, the most important molecules in living
organisms. They contribute to building many different
structures and parts and, as enzymes, control the
thousands of chemical reactions that maintain life
processes (Table 1.7).
This diversity of proteins can be explained by the way their subunits, the 20 amino
acids, are sequenced in various combinations. It is rather like arranging 20 kinds of
beads in different ways to make different necklaces of different lengths. The necklace
chains can then be arranged differently
in loops and folds to give each its
characteristic features.
Despite the diversity of proteins they
all have the same basic structure: up to
thousands of amino acids bond to form
linear polymers that are folded, twisted
or coiled. Plants can synthesise their
own amino acids but animals depend on
obtaining them from their diet. Well over
100 kinds of amino acids can be found in
cells but only 20 make up proteins.
Re vi e w
28 Relate the structure of lipid molecules to their function.
29 By means of a simple labelled diagram, distinguish between
saturated and unsaturated fats.
30 Where are phospholipids located in a cell?
31 Cholesterol is an important lipid molecule. What is its function?
32 Relate the structure of glycolipids to their function in the cell.
Figure 1.30 Linus Pauling,
US chemist and double
Nobel laureate.
26 Unit 3
Table 1.7 The functional diversity
of proteins
Types of Protein Function Examples
Motility Allow movement of cells and
their organelles
Tubulin forms microtubules to move agella, cilia, chromosomes and organelles.
Actin and myosin work together to move muscles.
Structural Provides support, strength
and protection
Collagen supports body tissues.
Fibroin makes a spider web stronger, weight for weight, than steel.
Keratin forms nails and hair.
Enzymes Catalyse biochemical reactions Catalase removes toxic hydrogen peroxide from cells by breaking it down into water and
oxygen.
All organisms have DNA polymerase, an enzyme that duplicates genetic information (DNA).
Transport Carry molecules from one
location to another or across
cell membranes
Haemoglobin carries oxygen to body cells.
Porin forms a hydrophilic pore in the outer membrane of mitochondria for the passage of
molecules.
Hormones Signalling between different
cell types; stimulation or
inhibition
Insulin travels in the blood and binds to cell receptors to trigger the uptake of glucose.
Follicle-stimulating hormone (FSH) stimulates the maturation and release of ova (female
gametes).
Cell-surface
receptors
Label cells as targets for
hormones, viruses, growth
factors, recognition of self,
transmission of nerve impulse
Insulin receptors bind insulin to trigger the uptake of glucose by the cell.
Rhodopsin in the retina membrane allows us to see dim light.
Major histocompatibility complex (MHC) markers allow the immune system to recognise self
so the body does not destroy its own cells.
Neurotransmitters Signalling between neurones Endorphins activate nerve receptors to alleviate pain or stress.
Enkephalins act as analgesics (pain relievers) and sedatives affecting mood and motivation.
Immunoglobulins Recognition of foreign
substances (antigens)
Antibodies cause foreign material to clump so it can be ingested by large white cells
(macrophages).
Poisons or toxins Chemicals for defence and to
aid in the capture of food
Red means danger. The castor oil plant produces the deadly toxin, ricin.
Snake venom contains many proteins that can paralyse and digest prey.
Figure 1.31 Proteins have a diverse range of functions. (a) Spindle bres attach to chromosomes in cell division.
(b) A spider web is composed of broin. (c) Haemoglobin carries oxygen to the cells in the body. (d) The castor oil
plant produces the deadly toxin, ricin.
a
b
c d
27
Chapter 1 The chemical
nature of the cell
Amino acids
Amino acids are small molecules that have the same basic structure a central carbon
atom to which are attached a hydrogen atom, a carboxyl acid group (COOH), an
amine group (NH
2
) and what is called an R group (Figure 1.32). It is the difference
in the R group that distinguishes one amino acid from another and gives each amino
acid its particular chemical properties. There are only 20 different amino acids found
in the proteins of living organisms (Figure 1.33).
Some R groups give the protein molecule polar regions and other groups make
regions non-polar. Non-polar hydrophobic regions are generally tucked away within
the protein molecule, away from the water molecules in the aqueous environment.
Polar and charged amino acids are hydrophilic. They tend to be on the surface of
protein molecules because of their afnity for the polar water molecules in their
environment.
Figure 1.32 Structural formula for
an amino acid, at about pH 7. An H
+
has
transferred from the COOH group to
the NH
2
group.
bioBYTE
The purpose of venom, a concoction of many digestive and toxic
proteins, is to kill prey and begin the digestion process, breaking
down tissues and muscles from the inside out. Spider and snake venom is
categorised as neurotoxic or cytotoxic. The Australian funnel-web spider
injects neurotoxic venom that directly affects the nervous system, causing
cramps, rigidity and paralysis.
Neurotoxins work by preventing neurons from communicating with each
other, but blocking nerve impulses does not always signify death. This ability
can be useful for humans in providing relief from pain. In response to injury or
inammation, cells release chemical messengers. These chemical messengers
alert pain receptors, which send signals to the brain. The brain interprets the
signals and we perceive pain. Analgesics work by either blocking the proteins
that receive signals that go to the brain or by interfering with the brains
interpretation of the signals.
Figure 1.33 The structural formulae of three of the 20 amino acids, grouped according to their properties:
(a) non-polar; (b) polar; and (c) electrically charged.
Figure 1.34 (above) This model of
haemoglobin shows hydrophobic
amino acids (brown) associating in
the centre of the molecule and the
hydrophilic (blue) amino acids tending
to interact with the surrounding
aqueous environment.
carboxyl
group
H
H
amine
acid
R
H
H
+
N

C

C

O

O
R group
a Non-polar

tryptophan (Trp)
H
3
N
+
C

C

H
CH
2
O
O

NH
b Polar
serine (Ser)
H
3
N
+
C

C

H
O
O

CH
2
OH
c Electrically charged
aspartic acid (Asp)
H
3
N
+
C

C

H
O
O

CH
2
C
O

O
From amino acids to proteins one step at a time
The process of synthesising protein molecules can be explained by the four different
levels that give rise to the nal structure.
28 Unit 3
hydrophobic
R group
interactions
ionic bond
CH
3
CH
3
CHCH
2
CH
3
CH
3
CH
3
CH
3
CH
0 HN

CH
2
OH 0
(CH
2
)
4
NH
+
3

0

CCH
2

O
CH
2
C

N

H



O

CH
2
O H H
CH
2


S

S


CH
2
COO

H
3
N
+
1 Primary structure
DNA determines the sequence of amino
acids in the polypeptide. Amino acids bond
together in the process of condensation
polymerisation and each bond between two
adjacent amino acids is called a peptide bond.
2 Secondary structure
Once the polypeptide chain is formed,
various parts undergo coiling and folding due
to hydrogen bonding between the various
amino acids that are present. Tight coils are
known as -helices and the folding forms
-sheets. Other parts of the polypeptide
chain remain unchanged and are called
random loops. -sheets and random loops
form the basis of the active site in enzymes,
being less rigid than -helices.
3 Tertiary structure
Hydrophilic R groups attract other hydrophilic R groups and hydrophobic
R groups attract other hydrophobic R groups according to the like attracts
like rule. These interactions between the R groups of the amino acids cause the
polypeptide chains to become folded, coiled or twisted into the proteins functional
shape or conformation. The interactions between the R groups of amino acids
result in hydrogen bonds, ionic bonds or disulde bridges between adjacent
cysteine amino acids. Protein molecules with the same sequence of amino acids will
fold into the same shape. A change to just one amino acid will alter the shape of
the protein molecule and it may not function properly.
Figure 1.35 (a) The order of amino
acids in the polypeptide is called the
primary structure.
(b) Coiling (-helices) and folding
(-sheets) result in the secondary
structure of a protein. Coils and sheets
are connected by random loops.
Figure 1.36
The specic function
of a protein is
determined by its
tertiary structure.
The tertiary
structure arises
from interactions
between R groups of
amino acids in the
polypeptide chain.
a
amino acid
-sheet
b
-helix
random loop
N
H
H
OH
C
O


N

C

C

H
H
R
O
polypeptide
backbone
-sheet
hydrogen
bonds
hydrogen
bonds
-helix
disulde bond
Chapter 1 The chemical
nature of the cell
29
a b
Kuru disease is a lethal disease which was found infecting women and children in
a tribe in Papua New Guinea in 1950. The infective agents are proteins that were
ingested when the tribe practised ritual cannibalism. They ate the brains of the
dead as a rite of mourning.
A number of infective agents consist of proteins. The human brain contains
cellular prion proteins, which occasionally can change spontaneously to an
abnormal form when part of the -helical structure converts to a -sheet
(Figure 1.37). This gives rise to a pathogenic or disease-causing condition resulting
in, for example, CreutzfeldtJakob disease. The changed protein alters other
proteins in the infected cell, creating a chain reaction in other cells.
Scientists believe that the pathogenic prion proteins form bres that kill
brain cells, creating tiny holes in brain tissue and giving it a spongy appearance
(Figure 1.38). Those affected start to lose their memories, their balance deteriorates
and they can die within 6 months.
Pathogenic prion proteins have been found in food products from cattle infected with mad cow
disease. These can similarly affect human brain tissue if ingested. Anyone who visited England during
the latest outbreak of mad cow disease cannot donate blood for 10 years after their visit as they may
have abnormal prion proteins circulating in their blood! Mad cow disease is thought to have originated
from cattle feed that contained the abnormal prion proteins of sheep infected with the disease scrapie.
It was a common practice to mix the unwanted components of slaughtered sheep into animal feed.
Describe changes to the secondary structure of prion proteins that leads to Creutzfeldt-Jakob
disease.
How do altered prion proteins affect the brain?
Eating diseased tissue that contains abnormal prion proteins can cause the brain to become
infected. Would you expect prion proteins to be small or large if they manage to enter the
bloodstream without being digested?
Would you recommend that steak be eaten rare or well done? Explain.
BIOBOX 1.7
PATHOGENIC PRION PROTEINS
Figure 1.37 (a) The structure of a healthy
cellular prion protein contains only -helices.
(b) The pathogenic form is created when
parts of the -helical structure change into
-sheets.
Figure 1.38 (below) (a) Healthy brain tissue.
(b) Brain tissue from a victim of Creutzfeldt
Jakob disease. Note the plaques (holes)
giving the brain tissue a spongy appearance.
a b
30 Unit 3
B
I
O
L
I
N
K
Protein structure
It is the tertiary structure that determines the function of the protein its
biological functionality. Some proteins form long, closely packed bres that are
insoluble in water and result in structural components of cells. Most proteins
form spherical or globular-shaped molecules that are soluble in water and perform
a variety of functional tasks.
4 Quaternary structure
Many large, complex protein molecules consist of two or more polypeptide
chains. Haemoglobin, for example, which carries oxygen in the blood, consists of
four polypeptide chains. A variety of hydrogen bonds, ionic bonds and covalent
bonds holds the polypeptide chains together and gives the overall shape to the
molecule.
Changing the nature of proteins
The function of protein molecules may change as a result of a number of factors,
apart from misreading the DNA code for proteins. Proteins may lose their functional
shape if they are exposed to high temperatures, strong salty solutions or very acidic
or alkaline conditions. These conditions can denature or change the shape of the
protein molecules. If the change is minor, the protein molecule can return to its
original shape, but if it is major, then it cannot.
Structural biologists use X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy to nd out
the structure of a protein that they are interested in. The techniques they use are time consuming and expensive
but they are effective in determining the spatial arrangement of the atoms that make up the protein molecules.
Specialised computer programs analyse the data the
biologists collect to determine the most likely conguration of
the amino acids of the protein. The research team then submits
the structure to a journal and to the Protein Data Bank, a
worldwide electronic library for processing and distributing
data about the three-dimensional structures of biological
macromolecules. This is an example of bioinformatics at work.
The public can access this information and view the three-
dimensional structure using a variety of computer visualisation
programs, such as Cn3D, which is free to download from the
National Centre for Biotechnology Information website.
What two methods are currently used by structural
biologists to nd the three-dimensional structure of a
protein?
What information is used by computer programs to
construct a three-dimensional representation of
protein molecules.
BIOBOX 1.8
FINDING THE SHAPE OF PROTEINS
Figure 1.40 Researcher with an x-ray crystallography machine
used to study the structure of proteins.
Figure 1.39 Raw and cooked egg.
The colourless protein of the white of
the egg albumen is changed by heat.
Chapter 1 The chemical
nature of the cell
Proteomics
A group of Australian scientists has used proteomics to develop a drug
to treat the u. Proteomics is a dynamic eld of research that looks at
the functions and interactions of proteins. The combined expertise of
computational biologists, mathematicians and molecular biologists has
resulted in the development of powerful tools, techniques and databases
for studying proteins.
It is estimated that there are approximately one million proteins at
work in the human body. Currently we know the structure of about 20 000
proteins from a range of organisms.
Where is proteomics leading us? Observing the three-dimensional
structure of proteins allows us to view the active sites of enzymes and the
binding sites of receptor proteins so that we can determine molecules that
will t into these sites. This can lead to the development of highly specic
drugs that will either stimulate the activity of the target or block its activity.
Australian scientists design life-saving drug!
Rational drug design describes the
approach to developing highly specic
drugs that will lock onto target structures
in this case a protein on the surface
of the inuenza virus particle and
prevent them from causing infection.
The approach depends on knowing the
structure of the target.
The u virus has a region on its
surface that is common to all strains of
the virus: a neuraminidase protein (N
protein for short). This N protein is used
by the virus to escape from host cells so that it can infect new host cells. An Australian
research team headed by Professor Peter Colman worked out the structure of the N
protein and then used computers to design a drug that would lock onto its active site
and prevent it from functioning. The virus was stopped in its tracks!
The drug is called Relenza.
What do studies in the eld of proteomics involve?
How is knowledge of the three-dimensional structure of proteins helping
scientists to design drugs?
What areas of proteins are targeted when designing highly specic drugs?
The drug Relenza, designed by Peter Colman and his team, stops the inuenza
virus from infecting new host cells. Describe how it does this.
BIOBOX 1.9
DESIGNER DRUGS
Figure 1.41 (a) This diagram by
Professor Peter Colman shows the
nine strongly conserved amino acids
that interact with sialic acid at the
active site of inuenza neuraminidase
protein. The asterisks mark the target
area for a drug designed to have a
stronger afnity for nearby amino
acids in the active site. (b) Stereo
model of sialic acid bound to the active
site of neuraminidase protein.
a
b
31
32 Unit 3
Nucleic acids information molecules
In 1869, Friedrich Miescher, a German doctor, extracted a white substance from the
nuclei of white blood cells that he collected from pus on soiled surgical bandages.
He called the substance nuclein. By 1900 the basic chemistry of this mysterious white
substance had been worked out. It was a long molecule made up of three distinct
chemical parts. Today this molecule is called nucleic acid. The name still suggests
Mieschers source of the substance.
Nucleic acids store information in a chemical code that directs the machinery of
the cell to produce proteins. Nucleic acids are every organisms genetic material; they
are the means by which the story of life extends through time and across all life forms.
Commonly recognised by the letters DNA (deoxyribonucleic acid) and RNA
(ribonucleic acid), nucleic acids are large, linear polymers that form when monomers
bond together. A molecule of DNA is composed of two long strands of subunits called
nucleotides, wound around each other to form the familiar double helix. RNA is
usually composed of a single chain of nucleotides and forms a single strand.
Nucleotides
Nucleotides are the monomers that make up these amazing nucleic acid molecules.
A nucleotide has three distinct chemical components:
1 a ve carbon sugar (ribose in RNA and deoxyribose in DNA)
2 a negatively charged phosphate group
3 an organic nitrogen-containing compound called a base (Figure 1.42).
There are four kinds of nitrogenous (nitrogen-containing) bases in DNA:
adenine (A)
thymine (T)
guanine (G)
cytosine (C).
In each nucleotide strand, the sugar molecule of one nucleotide binds to the
phosphate group of the next nucleotide, leaving the nitrogenous base sticking out
from each sugar and opposite the nitrogenous base of the second strand. Hydrogen
bonds between the opposing pairs of nitrogenous bases hold the double helix together,
much like the rungs of a twisted ladder or a spiral staircase. The bonding of the
nitrogen bases does not happen by chance: A bonds with T and C bonds with G,
giving rise to the base-pairing rule.
Re vi e w
33 Explain why there are so many different kinds of protein.
34 Relate the structure of proteins to their function.
35 Draw a concept map to illustrate the diversity of proteins.
36 Where in a protein molecule would you nd a hydrophilic amino
acid? Explain why some amino acids are hydrophilic.
37 Describe the two structural patterns that can develop to give a
polypeptide its secondary structure. Explain their formation.
38 What level of protein structure determines its function?
bioTERMS
DNA
(deoxyribonucleic acid) an
information molecule that
is the universal basis of an
organisms genetic material; it
contains instructions, written
in a chemical code, for the
production of proteins by the
cell
RNA
nucleic acid consisting of a
single strand of nucleotides;
plays an essential role in protein
synthesis (as messenger RNA
and transfer RNA) and as
a structural component of
ribosomes
nucleotides
the basic building blocks
of nucleic acids (DNA and
RNA) linked together by
phosphodiester bonds; each
nucleotide is made up of a
ve-carbon sugar, a phosphate
group and a nitrogen base,
being guanine, cytosine,
adenine or thymine in DNA; in
RNA, thymine is replaced by
uracil
gene
the basis of heredity; segment
of DNA that directs the
formation of a protein
genome
all of the genetic material
contained in an organism
or a cell; includes both the
chromosomes within the
nucleus and the DNA in
mitochondria
33
Chapter 1 The chemical
nature of the cell
The difference between the deoxyribose sugar of the DNA and the ribose
sugar of RNA is that ribose has one less oxygen atom. The nitrogenous base
thymine is also replaced by the base uracil (U) in RNA.
Nucleotides link together in what is called a 5 to 3 direction to form long
polymers. Translated this means that the phosphate group attached to the
5 carbon of one ribose monomer bonds to the hydroxyl group attached to
the 3 carbon of another ribose monomer, forming a particular bond called a
phosphodiester bond. In the process of polymerisation, the hydrogen from the
sugar and the hydroxyl from the phosphate condense out as a water molecule.
The function of DNA
The particular sequence of nucleotides in the DNA molecule forms a code
which, until 1966, had not been cracked. The code carried by the DNA is
organised in triplets (three nucleotides) that determine the order in which
the amino acids are sequenced and, in turn, this sequence determines which
protein is formed.
It sounds simple but when we consider that each cell of our body carries
well over a metre in length of DNA, twisted and coiled into 46 chromosomes
that have more than three billion base pairs (bp), it is not surprising that
there is such a diversity of proteins. However, not all the length of the DNA
molecule codes for proteins. The parts that code are the genes and the total
set of genes that each cell of an organism has is called its genome. The study
of these sets of genes and the way they interact with each other is called
genomics.
Figure 1.42 (a) DNA is made up of deoxyribose sugars and RNA of ribose sugars. (b) Nucleotides link together to form
a single-stranded DNA molecule. (c) The DNA helix is a double-stranded molecule. The two strands are held together
by hydrogen bonding between complementary nitrogenous bases.
deoxyribose (DNA)
a
c
HO CH
2
H
H
OH
H
OH
O
OH
H
ribose (RNA)
H OH
H OH
H OH
CHO
CH
2
OH
HO CH
2
H
H
OH
H
H
O
OH
H
H H
H OH
H OH
CHO
CH
2
OH
2
1
b
phosphodiester bond
nucleotide
G
T
C
A
O

O

P

O

CH
2
O
O

4
G C
A T
C G
G C
G C
G C
A T
A T
P
P
S
S
B B
B B
S
P
S
P
sugar/
phosphate
strand
nucleotide
base
hydrogen bonds
A/T T/A
C/G G/C
3 end
5 end
=
=
3
4
5
B
I
O
L
I
N
K
DNA
34 Unit 3
Figure 1.43 Watson and Crick with their DNA molecule.
Determining the structure of
DNA was the greatest biological
discovery of the 20th century.
It led to an understanding
of how genetic information
encoded within the molecule
passes from generation to
generation.
The discovery of the
double helix is not as simple
as it seems. The claim for
its discovery has been
contentious. Many years of
work and investigation by
scientists contributed to the
body of knowledge that
eventually led James Watson
and Francis Crick to produce
the famous model of the
double helix.
Watson and Crick
used X-ray images of the
DNA molecule made
by Rosalind Franklin to determine
its structure (see Figure 8.5). At rst it was thought that the molecule
consisted of one helix but eventually Watson realised that the molecule
was composed of two helices. Upon seeing an X-ray image of DNA
taken by Franklin, Watson wrote The instant I saw the picture my mouth fell open and my pulse began to race ...
the black cross of reections which dominated the picture could arise only from a helical structure.
Watson and Crick wrote of their discovery in a letter submitted to the editors of the
journal Nature in 1953, with the nalised details of the structure: We wish to suggest
a structure for the salt of deoxyribose nucleic acid (D.N.A.). This structure has novel
features which are of considerable biological interest.
Quite an understatement!
Why was the discovery of the structure of DNA so important?
Describe the experimental evidence that led to the realisation by Watson that DNA had a double-helix
structure.
When were the ndings of Watson and Crick rst published?
BIOBOX 1.10
DISCOVERY OF THE SECRET OF LIFE
B
I
O
L
I
N
K
Test yourself
35
Chapter 1 The chemical
nature of the cell
Re vi e w
bioTERMS
template
a molecule that serves as a
pattern for the generation of
another molecule (e.g. DNA is a
template for RNA synthesis, or a
single DNA strand serves as the
pattern or template for building a
new second strand)
P
R
A
C
T
I
C
A
L
A
C
TIVIT
Y
1
.
2
DNA consists of two complementary polynucleotide strands held together by
hydrogen bonds. If we know the nucleotide sequence on one strand, we also know the
nucleotide sequence on the other strand because we know which nucleotide bonds
with which. One strand is a template for the other strand.
DNA is the master code that determines the very nature of cells and therefore
of life forms. Owing to its unique ability to replicate, DNA is a semi-conservative
molecule (see page 208) that passes on this information from one generation of cells
to the next and from one generation of organisms to the next. Thus, it is an incredibly
signicant biomacromolecule.
The DNA of a cell is largely contained within the nucleus. Some DNA is found in
the mitochondria and in chloroplasts of cells. Its presence there has given rise to some
interesting ideas about how these organelles came to be tucked inside the cells.
Unlocking the DNA code and extraordinary advances in biotechnology have
meant that the DNA molecule can now be manipulated and modied. We live in a
time of designer proteins when the molecular products of cells can be changed and
possibly life forms too.
The function of RNA
RNA has many functions in producing proteins. RNA takes the information on the
DNA strand and creates the proteins necessary for life. This is called gene expression
the gene expresses itself by producing proteins.
The information on genes segments of DNA containing the codes for making
proteins is transferred to messenger RNA (mRNA). The mRNA molecule is
shorter than chromosomal DNA and is single stranded so that the molecule can
carry the code out of the nucleus and into the cytoplasm. This is where the protein-
making factories (ribosomes) are located. The ribosomes read the mRNA code
three nucleotides at a time, that is, in codons. Each codon signals the ribosome to
add specic amino acids to a growing protein chain. The ribosomes are composed
of ribosomal RNA (rRNA) and protein. The incoming amino acids are attached to
transfer RNA (tRNA) molecules. Each tRNA molecule has an anticodon that will
bind with a complementary codon on mRNA. This is how the ribosomes know the
correct amino acid to add to a growing protein chain. This process is explored in
depth in Chapter 8.
39 a Describe, by means of a simple annotated diagram, the structure of a nucleotide.
b What distinguishes one nucleotide from another?
40 Describe, using an example, what is meant by the base-pairing rule.
41 Where is DNA located in a cell? Describe its function and explain its signicance.
42 Using a table, compare DNA and RNA in terms of their structure and function.
43 Explain, by means of a concept map, the connection between gene, genome, protein and DNA.
44 Name the three RNA molecules involved in gene expression and the role each has in this process.
36 Unit 3
Visual summary

atoms
addition of
functional groups
carbon
hydrophilic elements
ionic
compounds
molecular
compounds
hydrophilic
Compounds
polar
molecules
The Cell A
Chemical Factory
triglycerides
non-polar
molecules
fatty acid chains
hydrophobic

lipids
oxygen nitrogen hydrocarbons hydrogen
biomacromolecules

monosaccharides
energy source

nucleotides

amino acids
complex
carbohydrates
nucleic acids
proteins
structural
components
specic biological
functions
37
Chapter 1 The chemical
nature of the cell
Key terms
-helix denature ion polymers
amino acid disaccharides ionic bond polypeptide
amphipathic disulde bridges ionic compounds polysaccharides
anion DNA isotopes proteins
atom electrolytes lipids proteome
autoradiography electron liposome proteomics
autotroph element macromolecules proton
-sheet enzyme molecular compounds radiation
bioinformatics formulae monomer radioisotope
biological functionality functional groups monosaccharides RNA
biomolecules genes neutron salts
buffer genome non-polar saturated
carbohydrate genomics nucleic acids semi-conservative
cation glycolipid nucleotides steroids
cell glycoprotein orbitals structural formulae
chemical bonds heterotrophs organic chemistry symbiotic
chemotroph hydrocarbons organic compound template
cholesterol hydrogen bond peptide bond tracers
compounds hydrophilic pH triglyceride
condensation polymerisation hydrophobic polar unsaturated
conformation intermolecular bonds polarity valence electrons
covalent bonds intramolecular bonds polymerisation
Apply understanding
Explain the concept of like dissolves like and the
signicance of this to molecules in cells.
Why is hydrogen bonding between water
molecules important to a 100-m tall gum tree?
Polymers result when bonds between monomers
are formed with the removal of water. Suggest a
way that the bonds between monomers could be
broken. Justify your answer.
All amino acids contain the same two functional
groups. How then do the 20 amino acids differ
from one another?
Why is nitrogen (N) considered to be an essential
element for all living things?
-Keratin is a brous protein that can be
stretched to about twice its length and is elastic.
Silk broin is also a brous protein but is not
elastic. Silk has great tensile strength and is much
stronger than hair. Explain these observations in
terms of the structure of their protein molecules.
Cellulose and glycogen have different physical
properties and biological functions but are both
polysaccharides made up of the same glucose
monomer. Explain these differences.
One strand of DNA consists of the base sequence
ATGCGTACTTAACC. Write the:
a sequence of bases for the complementary DNA
strand
b sequence of bases in an RNA copy of the
original DNA strand
Draw a diagram to show the orientation of
phospholipid molecules when placed in water.
Explain why this happens.
g Egg white is rich in the globular protein albumin.
When heated this liquid becomes a white opaque
solid. Using your knowledge of protein structure,
explain this observation.
38 Unit 3
Investigate and inquire
Water and paint thinner do not mix. Using
these two substances, design an experiment
that would determine whether another
substance called X is polar or non-polar.
Present your design as an annotated ow
diagram.
Identify three everyday products that are
largely made up of the polysaccharide cellulose
and relate their usefulness to the chemical or
physical properties of the molecule.
A restaurant owner has asked you to write a
brief report about the use of saturated fats
for frying rather than unsaturated fats. What
are the advantages and disadvantages of both
substances that may be of interest to the
restaurant owner?
You have been asked to suggest two treatments
for a permanent-wave process for hair. Find
out about the protein, keratin, that makes
up hair and explain how your two treatments
could result in hair being arranged into the
desired shape. (Hint: You will need to consider
a particular amino acid that makes up the
protein keratin.)
Use the National Centre for Biotechnology
Information (NCBI) website to search for
the gene coding for insulin. Write down the
rst 18 nucleotides in this gene and use a
genetic code to determine the primary protein
structure (six amino acids) that this segment
of DNA codes for. How would this DNA
sequence differ from the RNA sequence for
this gene?
Review this chapter to make up a list of the
various technologies and applications that have
resulted from our knowledge of biomolecules.
Select one and prepare a short presentation,
using library and Internet resources.
Carbon, hydrogen, oxygen, nitrogen,
phosphorus and sulfur account for more that
99% of the mass of living cells and combine
to form the organic biomolecules; proteins,
nucleotides, lipids and carbohydrates. The
elements in each class of biomolecules appear
in roughly the same proportions and assemble
to carry out similar tasks in all species. The
table below shows the relative composition of
elements in four biomolecules.
Element Percentage composition of elements
in four biomolecules
Bio-
molecule
A
Bio-
molecule
B
Bio-
molecule
C
Bio-
molecule
D
Carbon 30 25 23 32
Hydrogen 38 50 46 61
Oxygen 16 25 23 7
Nitrogen 14 0 7 0
Phosphorus 2 0 0 0
Sulfur 0 0 1 0
a Which of the biomolecules shown in the
table above is an example of a protein? Give
reasons to support your decision.
b Where in an animal cell would you expect
to nd high levels of biomolecule A?
Explain.
c Two students were arguing about
Biomolecule A. Rizky claimed it was a
single stranded molecule while Freya
insisted it was a double stranded molecule.
i Could they both be correct? Explain.
ii They conducted experiments and found
that the number of Guanine bases in
the molecule was exactly the same as
the number of Cytosine bases and the
number of Adenine bases was equal to
the number of Thymine bases. Whose
claim is supported by these results?
Explain.
iii A mature red blood cell from a human
was found to be lacking Biomolecule A
while a stem cell from the bone marrow
had high amounts of this molecule.
What conclusions can you draw about
these cells?
d A test was carried out on a patient suspected
of suffering from the glycogen storage
disease known as Pompes disease. In this
disease, sufferers lack the enzymes required
to break glycogen down into glucose.
Which of the Biomolecules listed above
would be in elevated levels if the diagnosis
returned positive? Explain.