THEME

A Unity and diversity

1 Molecules
 Water A1.1

• This is DNA, one of the molecules classi ed as a nucleic acid and a molecule that
is integral to life on Earth. The molecules that are important to life are diverse and
complex. Yet their basic structures are largely consistent from species to species. This
allows us to study the fundamental structures and functions of these molecules and
apply that knowledge to all living organisms. In this chapter, you will first study the
solvent of all biochemically important molecules, water. Later, you will consider the
structure of nucleic acids.

A1.1 Water

Guiding Questions
What physical and chemical properties of water make it essential for life?
What are the challenges and opportunities of water as a habitat?

What makes water essential for living organisms? What physical and chemical
properties does water have that provide essential benefits to aquatic, marine and
terrestrial organisms? What opportunities and challenges does water pose for life?
These are not questions designed to be answered in one or more short statements.
They are questions that deserve to be explored. A portion of this chapter will attempt
to begin that exploration.
Life first evolved in water and all living things are still dependent on this amazing
molecule. Fortunately, we live on a planet where water exists in all three states: there is
abundant liquid water, water vapour and ice. Water, as a polar molecule, is an excellent
solvent for the vast majority of elements and compounds necessary for life. Water
molecules are found inside and outside cells, and chemical communication in and out
of cells must occur in a water environment.

Water has both advantages and disadvantages for the aquatic and marine organisms
that use it as a habitat. Advantages include the fact that water provides buoyancy and
stable thermal properties for these organisms. Disadvantages include its relatively
high viscosity compared to air. This means that many organisms living in water have
adapted their body shape and propulsion mechanisms in order to move easily through
an aquatic environment.

A1.1.1 - The medium of life

A1.1.1 - Water as the medium for life
Students should appreciate that the first cells originated in water and that water remains the
medium in which most processes of life occur.

Life on Earth has never been possible without water. Imagine a primordial planet
slowly cooling from its original molten mass. That primitive Earth would not have had
any water because of the extremely high temperatures at its centre and on its surface.

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 A UNITY AND DIVERSITY Molecules

The surface of the Earth may

have looked like this early in
its history, with magma giving
off tremendous heat at the
surface.

The origin and evolution of the first cells could not begin until temperatures cooled
i
Approximately 70% of
our planet's surface is enough for water to form and, later, for the water cycle to begin. We take for granted
covered by water. The
the changes that water makes as it goes between its solid, liquid and gaseous phases.
deepest parts of the
Earth's varied temperatures allow these changes. That was not the case in our planet's
Paci c Ocean are deeper
than the height of the early history.
highest land peaks.
It is thought that the first cells formed and slowly evolved in the oceans. Cells require a
complex series of biochemical reactions. This means a solvent is needed for reactions
Every solution
where water is the
to occur. Ocean water provided the source for that solvent. The first cells evolved a
solvent is called an membrane to separate the water in the cytoplasm from the "ocean water".
aqueous solution.
Thus, cytoplasm, When most people think of water, their first thoughts are about the water they
rivers, blood and drink and bathe or swim in. But water is more widespread than that. Below are a few
oceans are all examples of where the importance of water as a solvent is vital to living organisms.
aqueous solutions.
Water is the solvent that:
Challenger Deep (the
lowest known portion
of the Mariana Trench)
i • makes up the fluid (cytoplasm) in all cells where all cellular reactions occur
• makes up the fluid inside all organelles in cells
is 10,984 m below the • is found between cells of multicellular organisms (intercellular or tissue fluid)
surface of the Paci c
Ocean. Mount Everest
• permits transport of substances into and out of cells
(the tallest known land • is essential to blood and many other body fluids in humans and other organisms
mass) is 8,848 m above • provides the medium in which all organisms in oceans, lakes and rivers live.
sea level. The difference
between those points is
over 19 km or 12 miles. Nature of Science
Measurements in science often change over time. If you research the world's
deepest and tallest points you may find slightly different numbers (metres
below and above sea level). There are various possible reasons including: how
recently the data point was taken; what method was used to obtain the data;
whether or not the data change over time due to natural causes. Can you think
of other reasons for the data to vary?

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 Water A1.1

A1.1.2 - The structure and polarity of water

molecules

A1.1.2 - Hydrogen bonds as a consequence of the polar covalent bonds within water
molecules
Students should understand that polarity of covalent bonding within water molecules is
due to unequal sharing of electrons and that hydrogen bonding due to this polarity occurs
between water molecules.
Students should be able to represent two or more water molecules and hydrogen bonds You may be used
between them with the notation shown below to indicate polarity. to seeing the Greek
symbol A called delta.
05- A is the capital letter
symbol and & is the
H&+ H°+ corresponding small
case letter symbol for
delta.
To understand the properties of water and its importance to living organisms, it is
necessary to understand the molecular structure of water molecules.
The electrons being
• A1.1 Figure 1 This image shows the covalent bonds in a shared to create the
water molecule. Each of two hydrogen atoms is bonded at covalent bonds within a

an angle to a single oxygen atom. Remember that each of water molecule are not
the two covalent bonds is a pair of shared electrons. being shared equally
between the two

The covalent bonds between the oxygen atom and the two hydrogen atoms of a water atoms. In Figure 1, you
see the symbols &+ and
molecule are categorized as polar covalent bonds. 8 (delta positive and
delta negative). These
You may remember from fundamental chemistry that covalent bonds form when two symbols represent
atoms share electrons. Electrons are negatively charged and the nucleus of an atom is areas of low or high
positively charged (because of the protons). So, any equally shared electrons create a electron density in the
non-polar covalent bond. This is because neither of the atoms has a higher density sharing of electrons to
create a covalent bond.
of electrons than the other. Good examples of non-polar covalent bonds include the Each hydrogen atom is
covalent bond between two carbons and the covalent bond between two hydrogens. assigned a 8* because
that is an area of lesser
Polar covalent bonding results from an unequal sharing of electrons. In water, the single electron density (thus

oxygen atom is bonded to two different hydrogen atoms. Each oxygen-hydrogen bond a small positive charge
due to the single
is a polar covalent bond. This results in a slight negative charge at the oxygen end of the
proton of the hydrogen
molecule and a slight positive charge at the end with the two hydrogens. atom). The oxygen
atom is assigned a &-
Because of the open triangular shape of a water molecule, the two "ends" of each charge due to its high
molecule have opposite charges. The oxygen side is slightly negative and the hydrogen electron density.

side is slightly positive. This is why water is a polar molecule: it has different charges at
each end. Because of this, water molecules interact with each other and other molecules Practise sketching from
SKILLS
in very interesting ways. Many of these interactions are explained by the usually short- memory a diagram
lived (ephemeral) attractions between either two water molecules or between a water similar to the one
shown in Figure 2.
molecule and another type of charged atom (or ion). These ephemeral attractions are Include the hydrogen
called hydrogen bonds and will be explained further in the following sections. bond and the delta
symbols and charges as
A1.1 Figure 2 Two water molecules showing a single shown. Practise adding
hydrogen bond between them. The bonding force of
8+, a third and fourth water
each hydrogen bond (indicated by the dotted line) is
molecule with the
weak. In liquid water, the bond is ephemeral because
same symbolism and
the water molecules continue to move around.
orientation.

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A UNTY AND DIVERSITY Molecules

A1.1.3 - Cohesion of water molecules

A1.1.3 - Cohesion of water molecules due to hydrogen bonding and consequences for
organisms

Include transport of water under tension in xylem and the use of water surfaces as habitats
due to the effect known as surface tension.

Water molecules are highly cohesive. Cohesion occurs when molecules of the same type
are attracted to each other. As you have seen, water molecules have a slightly positive
end and a slightly negative end. Whenever two water molecules are near each other,
the positive end of one attracts the negative end of another - this is hydrogen bonding.
When water cools below its freezing point, the molecular motion of the water
molecules slows to the point where the hydrogen bonds become locked into place
and an ice crystal forms. Liquid water has molecules with a faster molecular motion,
and the water molecules are able to influence each other, but not to the point where
molecules stop their motion. This influence is highly important and leads to many
of the physical and chemical properties of water. The ephemeral hydrogen bonding
between liquid water molecules explains a variety of events, including the following.

• Why water has a surface tension. Surface tension is due to the fact that
You can float a
paperclip on water the layer of water molecules at the surface of a body of water does not have
because of the molecules of water above it. Because of this, the water molecules show a
surface tension of the relatively strong cohesive force to the molecules immediately around and below
water. Make sure you
maximize the surface
them (no molecules are pulling upwards). This surface tension must be broken
area of the paperclip on in order for an object to move through the surface from above. It is surface
the water if you try this. tension that causes you pain when you do a "belly flop" into a body of water.
It is also surface tension that creates a habitat for some animals such as water
striders and basilisk lizards.
A green basilisk (Basiliscus
plumifrons) (found in Central
America) running across the
surface of water. Aided by its
webbed feet to increase the
surface area in contact with
the water, the lizard must keep
running in order to not break
through the surface tension.

6
 Water A1.1
Think of a xylem tube
• How water is able to move as a "water column" in the vascular tissues of plants.
and the upwards
The majority of water moving upwards in a plant moves within small tubes movement of water
called xylem. Think of xylem as being similar to numerous tiny straws. When as being similar to
water evaporates from a leaf (in a process called transpiration) the water that what happens when
evaporates in order to exit the leaf has cohesion to the water in a xylem tube you use a straw in a
drink. The suction you
that adjoins the exit point. The evaporation with corresponding cohesion
provide creates tension
creates a low pressure in this area called tension. This tension pulls on the other (low-pressure pressure
water molecules in the xylem tube so they all move upwards towards the leaf. area at the top of the
The molecules are all cohesive to each other and all move up collectively. This straw) and the fluid is
evaporation occurs in small, controlled openings called stomata, which are moved upwards along
the straw. The bottom
usually found on the underside of leaves. The water that transpires from the leaf
of the straw in your
is replaced in the xylem in the root system of the plant. drink is similar to the
bottom of the xylem
An example of the importance
tubes found in the root
of cohesion. At the top, water is
system of a plant.
evaporating from a stoma (singular
of stomata). Stomata are very small
openings that can be opened or closed
and are found primarily on the under
surface of leaves. The evaporation of
water from open stomata is called
transpiration. The water is provided
to the leaf by many xylem tubes. The
transpiration of water creates tension
(a low-pressure area in the leaf and
xylem tube) and the polarity of water
molecules pulls the entire water
column to move towards the low-
pressure area. The xylem tube within
the leaf is continuous with the xylem in
the stem and root. The water moving
upwards is replaced by ground water
moving into the root system.

A1.1.4 - Adhesion between water and other

polar substances
A1.1.4 - Adhesion of water to materials that are polar or charged and impacts for
organisms

Include capillary action in soil and in plant cell walls.

Water molecules are certainly not the only molecules in nature that exhibit polarity. Cohesion and
An attraction between two unlike molecules due to hydrogen bonding is called adhesion are both a
adhesion. When water molecules are attracted to cellulose molecules by hydrogen result of the polarity
bonding, the attraction is an example of adhesion because the hydrogen bonding is of water molecules.
Cohesion is an
between two different kinds of molecule. Where is this important in nature?
attraction between
two water molecules
• Water within the xylem. Cohesion and adhesion are both at work in this
and adhesion is an
example. When the column of water is "pulled up", cohesion moves each attraction between
molecule up; when the column is not being "pulled up", adhesion keeps the a water molecule
entire column from dropping down within the tube. The same phenomenon and another polar
occurs when water is placed in a capillary tube - you can think of the xylem molecule that is not
water.
tissue in plants as being biological capillary tubes.

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 A UNITY AND DIVERSITY Molecules

A capillary tube is a glass tube

(similar to a straw) that has a
very narrow inside opening.
In this photo, a capillary
tube has been inserted into
a vessel lled with water with
a red dye. The liquid will
spontaneously climb upwards
into the capillary tube due
to adhesion and remain in a
fixed position within the tube.
The adhesion is the attraction
between the inside surface
of the glass tube and water
molecules.

• Capillary action in soil. Even soil that appears to be dry contains water in
How do the various
intermolecular forces microscopic channels. These small channels act in a similar way to capillary tubes.
of attraction affect Water molecules adhere to the polar molecules making up the soil and other
biological systems? water molecules are then sometimes moved by cohesion. The small root hairs of
plants intrude into the water-filled spaces and water is taken into the root.

A1.1.5 - The solvent properties of water

A1.1.5 - Solvent properties of water linked to its role as a medium for metabolism and
for transport in plants and animals
Emphasize that a wide variety of hydrophilic molecules dissolve in water and that most
enzymes catalyse reactions in aqueous solution. Students should also understand that the
functions of some molecules in cells depend on them being hydrophobic and insoluble.

As you have seen, water is a polar molecule and thus a polar solvent. In nature, water
is almost always found as a solvent carrying one or more of a wide variety of other
substances as solutes. Any solution that has water as the solvent is called an aqueous
solution. Any substance that dissolves readily in water is described as hydrophilic
(water loving) and any substance that does not dissolve easily is called hydrophobic
(water fearing).

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 Water A1.1
Hydrophilic molecules
The cytoplasm of a cell is a good example of an aqueous solution and contains a wide
variety of water-soluble substances. These hydrophilic solutes include (among others) The billecursin its
glucose, ions, amino acids and proteins. Some of the dissolved proteins in cells are the cytoplasm and also
biological catalysts called enzymes. Reactions within the cytoplasm depend on enzymes within membrane-
bound organelles
to proceed at a rate necessary for life and at a temperature tolerated by that type of cell.
such as the nucleus
and mitochondria.
Water is an excellent medium for transporting dissolved substances. The water
The uids of
contained in xylem vessels of plants is not pure water. It is an aqueous solution that these cellular
transports inorganic ions such as sodium, potassium and calcium. These and many environments use
other essential substances are hydrophilic; they dissolve easily in water and are water as a solvent
transported upwards from the root system to the leaves. because most
biochemically active
The blood of many animals, including humans, is also an aqueous solution. The red molecules are polar
and dissolve easily in
and white blood cells are suspended in plasma. Plasma is an aqueous solution of an
an aqueous solvent.
incredible array of molecules. Anyone looking at the results of a typical medical blood
test can see the variety of solutes in this solution.

'ASSIUM 16 A small section of the

1.04 results of a human blood

test showing some of the
RBON DIOXIDE
LORIDE 15 dissolved substances in the
aqueous portion of blood
LEA NITROGEN 6.1 called plasma.
REATININE 3. 0
UN/ CREATININE RATIO 9.7
JRIC ACID
PHOSPHORUS 64
CALCIUM 3.7

HDL CHOLESTEROL
CHOLESTEROL, TOTAL
LDU CHOL, CALCULATED
CHOLESTEROL/HDL RATIO 11'

See footnote 1
-ANDTDES
Hydrophobic molecules
Some non-polar (insoluble) molecules found in nature are important to living
organisms. Here are some examples.

• Steroid hormones, such as ostradiol and testosterone, are able to pass directly
through the plasma membrane and nuclear membrane of a cell. Steroid
hormones can do this because they are hydrophobic and are able to pass
directly through the hydrophobic layers of cell membranes.
• Many proteins have some sections that are hydrophilic and other sections that
are hydrophobic. Membrane-bound proteins may use one or more hydrophobic
areas to embed into the hydrophobic layers of a membrane while their
hydrophilic sections) extends into either the intercellular fluid or cytoplasm.
This enables the protein to stay attached to the membrane but still interact with
soluble substances in the surrounding cell fluids.

9
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A UNTY AND DIVERSITY Molecules

• The epidermal cells of leaves are capable of secreting a wax that is used to coat
the leaves and is called the cuticle. This wax cuticle is hydrophobic and acts as a
barrier to water entering and especially exiting the leaf by evaporation. Without
this cuticle, leaves would quickly dehydrate because their function requires a
thin, broad surface area exposed to the Sun.

A1.1.6 - The physical properties of water

A1.1.6 - Physical properties of water and the consequences for animals in aquatic
habitats
Include buoyancy, viscosity, thermal conductivity and specific heat. Contrast the physical
properties of water with those of air and illustrate the consequences using examples of
animals that live in water and in air or on land, such as the black-throated loon (Gavia arctica)
and the ringed seal (Pusa hispida).
Note: When students are referring to an organism in an examination, either the common name or the
scientific name is acceptable.

Table 1 outlines the important physical properties of water compared with air.

Property Water Air

Buoyancy or Buoyant force equals the weight of An object placed in air has an almost
buoyant force the water displaced by the object. Theinsignificant buoyant force. This
(an upwards buoyant force is upwards because force is equal to the weight of the air
force exerted there is more pressure from below (in displaced by the object.
on an object the water) than above (in the air).
placed in the
medium -
either water
or air)
Viscosity Water's resistance to an object Air's resistance to an object moving
moving through it. through it. Since air is far less dense
than water, air's viscosity is far less.
Thermal The ability of a substance to transfer The thermal conductivity of air is
conductivity heat. Water has a high thermal very low compared to water.
conductivity.
Specific heat In simplest terms, water can absorb Air's ability to absorb or give off heat
capacity or give off a great deal of heat without without changing temperature is very
changing temperature very much. low compared to that of water. The
Think of a body of water on a very temperature of the air changes easily
cold night: even though the air may and rapidly due to weather events.
be very cold, a nearby body of water
is relatively stable in temperature.

A1.1 Table 1 Physical properties of water

The physical properties of water have important consequences for animals that live
in aquatic habitats, such as the black-throated loon (Gavia arctica) and the ringed seal
(Pusa hispida).

10
 Water A1.1
The black-throated loon is a beautiful bird that lives
primarily in very cold regions of the Northern
Hemisphere. As with most aquatic birds, the loon
transfers regularly between land (for nesting), water (for
feeding) and air (for flying). Even though this bird is
capable of diving for food, it spends much of its time in
water on the surface relying on the buoyant force of the
water to float. The bird requires energy to overcome the
viscosity of water to move across the water surface and
even more when it dives for fish and other food sources
below the surface. Webbed feet and efficient, streamlined
body shape aid the loon in this movement. When the
bird is in water, the high thermal conductivity of the
water would cause the loon to lose more body heat than Black-throated loon
when it is in the air. Like many waterbirds, loons use an adaptation to prevent (Gavia arctica).
this. They have an oil gland near their tail and they use their beaks to rub this oil
over their feathers to make them waterproof. When the air is very cold (below You are not required to
1°C) the surrounding water is likely to be warmer than the air because the high memorize the scientific
specific heat of water allows its temperature to remain relatively stable in names (genus and
species) of example
comparison to air. organisms.

The ringed seal is another animal that is common in cold environments of the
Northern Hemisphere. This small seal is buoyant, although not as buoyant as a Melting sea ice due
to global warming
loon - less of its body is above the surface of the water when resting. It is buoyant
is threatening many
enough to keep its snout above water easily and thus has an easily available supply species, including seals,
of air. Seals spend a great deal of time swimming in and under the water to catch because their habitats
food (fish and invertebrates) and occasionally to escape a predator such as an are fundamentally
changing in a very
orca. Their streamlined shape and paddle-like feet are great assets in overcoming
short period of time
the viscosity of water. But water has high thermal conductivity compared to air, No one country by
so ringed seals need to minimize body heat loss. They do this by having a thick itself can solve the

blubber under their skin. The blubber is insulation and reduces heat loss from problem of global

the seals' internal organs. Like the black-throated loon, ringed seals are protected warming.
from very low air temperatures by the relatively high temperature of arctic water
(compared to arctic air) which is due to the high specific heat of water. What biological
processes only happen
at or near surfaces?

Ringed seal (Pusa hispida).

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A UNTY AND DIVERSITY Molecules

HL

A1.1.7 - The origin of water on Earth

A1.1.7 - Extraplanetary origin of water on Earth and reasons for its retention
The abundance of water over billions of years of Earth's history has allowed life to evolve.
Limit hypotheses for the origin of water on Earth to asteroids and reasons for retention to
gravity and temperatures low enough to condense water.

Earth has excellent conditions for retaining its large volume of water. As stated
previously, approximately 70% of the surface of Earth is covered by water and some
of that water is very deep. Earth's temperatures allow water to change phases readily,
but most remains as liquid water. In addition, our planet is large enough to have a
gravitational pull to retain water on or near its surface. Some of the water that helps form
our planet is almost permanently trapped deep in the crust. Temperatures deep in the
Earth are tremendously high but there are a few opportunities for this water to escape.

Castle Geyser in Yellowstone

National Park erupts once
every 14-18 hours. The
discharge of water is due
to underground magma
superheating water partially
trapped in the crust. There
are only a few areas on Earth
where water deep in the crust
can escape this way.

Water molecules exist in two forms. The difference between the two forms is the number
of neutrons in the nucleus of the hydrogen atoms of the molecule. Typically, water
contains "ordinary" hydrogen atoms without any neutrons. "Heavy water" contains
hydrogen atoms that have a neutron. This hydrogen is called deuterium. All bodies of
water contain a mix of these two forms, with typical water (no neutrons) being much
more common. When researchers calculate the ratio of hydrogen to deuterium in the
water of the oceans they get a ratio that is very similar to the ratio found in many asteroids.

12
 Water A1.1
Nature of Science The water contained
within asteroids is
Several countries currently have space craft that are tracking near-Earth not liquid water. The
asteroids, some of which are known to contain a great deal of water. In water is in the form
of hydrated minerals.
addition, several land-based telescopes are also tracking other near-Earth
These are solid
asteroids attempting to pick up signals showing the presence of water. From
this and other work it has been estimated that near-Earth asteroids may mined alsoned to
contain as much as 400 billion to 1,200 billion litres of water. water molecules or its
components.

A common theory is that farth he arcarly stage where the surface was hothied other.
Over very long periods of geological time as the Earth cooled, numerous asteroids
struck the Earth bringing hydrated minerals that released water, becoming part of the
Earth's crust. Our planet's early history had many more asteroid collisions because of
the unsettled time period of our early solar system and there were many millions of
years in which the collisions could have occurred.

Artist's rendition of a large

asteroid striking Earth.

i NASA is pairing
with some private
companies to send
an exploratory craft to
an asteroid named 16
Psyche. This asteroid
is about the size of the
state of Massachusetts
and is found in an
asteroid belt between
Mars and Jupiter. 16
Psyche is primarily
a metallic asteroid
and is projected to
contain as much as
10,000 quadrillion
Nature of Science US dollars-worth of
valuable minerals. The
The asteroid theory for the existence of water on Earth is not the only scientific rst unmanned mission
explanation. Some researchers believe that comets were a more important will be exploratory
origin. Others believe that hydrogen was trapped in the original cloud of only, but it is expected
that later missions
materials that formed the planet. The data is not conclusive for any one theory.
could focus on mining
Researchers will continue to add data and it is likely that a firm explanation will operations for gold
emerge over time. That is the way science approaches complex questions. and other valuable
substances.

A1.1.8 - The search for extraterrestrial life

A1.1.8 - Relationship between the search for extraterrestrial life and the presence of water
Include the idea of the "Goldilocks zone".

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A UNITY AND DIVERSITY Molecules

Any planet that could possibly support life must have water. Like Earth, that planet must
exist in an area of its solar system that would allow water to exist in its liquid form. This
position of Earth in relation to the Sun is called the habitable zone or Goldilocks zone.

Earth is in an orbit that is nearly perfect for water retention to occur. There are suitable
temperatures for water to exist as a liquid and sufficient gravity for retaining this water. In
addition, Earth is of a size that allows a suitable gravitational pull to enable water to remain
on and just under the surface. Earth has also developed an atmosphere and magnetic field
that protects it from most harmful ionizing radiation being emitted from the Sun.

Collectively, these are rare but necessary conditions for a planetary body to be
classified as being in a Goldilocks zone. Our galaxy, the Milky Way, is huge. It has
approximately 100,000 million stars possibly acting as the centres of solar systems.
The Hubble Space Telescope has shown that our galaxy is only one of 125 billion
galaxies in the known portions of the universe. Considering these prodigious numbers
of stars, it is reasonable to conclude that Earth is not the only planet in our galaxy or
universe that has the conditions necessary to support water and thus life.
This illustration compares X-RAY. RELATIVE
HABITABLE ZONE SIZE
ABUNDANIE;
three types of star: yellow G
stars (like the Sun), orange K
1000
dwarf stars and red M dwarf
stars. It shows the relative
sizes of habitable zones for
each type of star as well as
the relative X-ray radiation,
their relative abundance and
expected star longevity.

The possible existence of water is not the only factor that influences the possibility
of life evolving on a planetary body. Our Sun is one of the rarer star types that exist.
It is classified as a G type star based on its size and the radiation given off. Two more
abundant star types are types K and M. Each of these give off much more radiation than
a G star and that radiation would be harmful to life. Notice that K and M stars have a
Goldilocks (habitable) zone that is much smaller than a G star like our Sun.

HL end

Guiding Question revisited

What physical and chemical properties of water make it essential for life?

In this chapter we have described how and why water has:

• polar covalent bonds due to an unequal sharing of electrons between oxygen

and hydrogen
• cohesive forces attracting one molecule of water to another
• adhesive forces attracting molecules of water to other types of polar molecules
• excellent solvent properties for other polar molecules (solutes)
• properties making water the "solvent of life" as exhibited by cytoplasm, intercellular
fluids, blood and many other solutions that are vital to living organisms.

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 Water A1.1
Guiding Question revisited
What are the challenges and opportunities of water as a habitat?

In this chapter we have investigated:

• physical and chemical properties of water that provide both opportunities and
challenges for living organisms
• buoyancy - important to all aquatic and semi-aquatic organisms to keep
them at or near the water surface
• viscosity - the body shape and propulsion mechanisms of animals have
become adapted to overcome this resistance that water has for objects
moving through it
• thermal conductivity - organisms living in cold-water environments must have
either a physiology adapted for that water temperature or a means of insulation
from the cold because water readily conducts heat away from an organism's body.
• specific heat - water in oceans, lakes and rivers has a very high specific heat that
protects many aquatic organisms from much colder surrounding air temperatures

HL
• how water is necessary for life and very few planetary bodies possess conditions
necessary to retain water
• surface temperatures must allow water to exist in liquid form
• sufficient gravity must exist to prevent water from escaping.

HL end

Exercises
Q1. Describe how a polar covalent bond differs from a non-polar covalent bond.
Q2. Describe the pathway and the forces involved in getting water from the soil
surrounding a large tree to a leaf in one of the uppermost branches of that
tree (hint: start with the leaf).

Q3. State:
(a) an example of a molecule that is soluble in the cytoplasm of a cell
(b) the function of that same molecule.
Q4. State:
(a) an example of a molecule that is insoluble in the cytoplasm of a cell
(b) the function of that same molecule.
Q5. Describe two adaptations that the black-throated loon (Gavia arctica) has
evolved for overcoming the viscosity of water.

Q6. HL State three of the conditions necessary for a planetary body to be

classified in the Goldilocks zone.

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A UNTY AND DIVERSITY Molecules

A1.2 Nucleic acids

Guiding Questions
How does the structure of nucleic acids allow hereditary information to be
stored?
How does the structure of DNA facilitate accurate replication?

The organisms alive on Earth today have a long history and a very long family tree.
Living things do not just appear, rather they are descended from previous generations.
This is based on genetics. The information that is being passed from one generation
to the next is in the form of DNA. Humans have 46 DNA molecules in each cell in the
form of chromosomes. Written in the genetic code of DNA is information that makes
a blue whale what it is and makes you what you are.

Along the length of DNA molecules there are chemical messages that code for specific
proteins. Most of these protein messages are common to a species, but a few are
individual to one single individual of that species. Thus, each living organism is unique.
Preceding every cell division, the DNA replicates in an amazingly accurate series of
steps that produces two DNA molecules where there was once one. Life has continued
in this way for millions of years.

This chapter will introduce you to DNA and other molecules termed nucleic acids.
Nucleic acids include DNA and three types of RNA that are all involved in the synthesis
of proteins in cells.

A1.2.1 - DNA is the universal genetic material

A1.2.1 - DNA as the genetic material of all living organisms
Some viruses use RNA as their genetic material but viruses are not considered to be living.

Deoxyribonucleic acid (DNA) is the molecule that provides the long-term stored
genetic information for all organisms on Earth. When mutations occur that influence
evolution, they happen within DNA and are passed on to the next generation. The fact
that DNA is universal to all living organisms is evidence of our common ancestry, even
back to when the most complex life forms were single cells living in the oceans.

In addition to sugars and phosphate groups acting as a structural framework, DNA has
within it four nitrogenous bases: adenine, thymine, cytosine and guanine, which are
found along the length of the very long molecule. These four bases can be combined
in a tremendous variety of orders and lengths. The sequences of nitrogenous bases are
the genetic messages or genes. The messages are codes for amino acids. Amino acids
are the "building blocks" of proteins, and a cell's identity and function is determined
by the proteins it is able to synthesize. Every cell in a multicellular organism has the
same DNA, but each different type of cell only uses the genetic information that is
appropriate for that cell.

16
 Nucleic acids A1.2
An artist's rendering of the
interior of a cell showing
viral particles and a DNA
molecule. The spikes on the
viral particles are modi ed
proteins that attach to the
cells of an organism they
infect. Inside each of the
viruses is a nucleic acid, either
DNA or RNA (ribonucleic
acid), that may undergo one
or more mutations upon
every replication cycle. Some
mutations may alter the
proteins on the spikes and
change how well the protein
spikes attach to the host cells.

Viruses are not living organisms. Some viruses contain RNA as their genetic
information and some contain DNA. No matter which nucleic acid acts as the
genetic code for viral proteins, viruses are not considered to be alive because
they cannot survive without a cell of a living organism, and they have no internal
biochemistry when they exist as a separate particle. Only when they infect a
cell will their nucleic acid (RNA or DNA) become active and use the internal
biological components of the cell for their own uses. A virus has absolutely
no other function other than to reproduce itself: viruses exist to reproduce.
Sometimes that reproduction damages cells to the point of causing great harm to
the host organism.

A1.2.2 - The structure of nucleotides

A1.2.2 - Components of a nucleotide
In diagrams of nucleotides use circles, pentagons and rectangles to represent relative positions
of phosphates, pentose sugars and bases.

Both DNA and RNA are polymers of nucleotides. This means that both DNA and

Be have desting in stalled or evides within the min arget molecule So. in
first start with the structure of the nucleotides. Individual nucleotides consist of three
major parts: one phosphate group, one five-carbon monosaccharide (also called a
pentose sugar) and a nitrogenous base. Covalent bonds occur at specific locations in
order to produce a functional unit.

17
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A UNTY AND DIVERSITY Molecules

It is important to note phosphate , ОН ribose sugar or

that in Figure 1 a circle group HO deoxyribose sugar
is used to represent a
phosphate, a pentagon 1 of 4
is used to represent
a pentose sugar, and
a rectangle is used to nitrogenous base
represent a nitrogenous
base.

- base
pentose

A1.2 Figure 1 Two representations of a single nucleotide are shown in the diagram. The upper
drawing shows more detail, although not every atom and bond are shown of the pentose sugar and
only a bonding location is shown for a nitrogenous base. The lower drawing shows the level of detail
the IB requires you to draw from memory.

only phosphate group

bonded to one nucleotide only
A1.2.3 - Sugar to phosphate "backbone" of DNA
covalent bond and RNA
within a nucleotide

A1.2.3 - Sugar-phosphate bonding and the sugar-phosphate "backbone" of DNA

and RNA
_ covalent bond Sugar-phosphate bonding makes a continuous chain of covalently bonded atoms in each
between nucleotides strand of DNA or RNA nucleotides, which forms a strong "backbone" in the molecule.

Nucleotides in both DNA and RNA bond together to produce long chains or polymers.
In order to form a chain of nucleotides, the pentose sugar of one nucleotide is
covalently bonded to the phosphate group of the next nucleotide. This means that
there will always be one phosphate group with only one bond to a sugar at one end of
the nucleic acid polymer, and a pentose sugar with only one bond to a single phosphate
at the other end.

only pentose sugar

bonded to one
nucleotide only • A1.2 Figure 2 Some nucleic acids are formed from a single chain of nucleotides.

18
 Nucleic acids A1.2

Challenge yourself
Examine Figure 1 on the previous page. Notice that the carbons of the pentose
sugar are numbered. Now look at Figure 2, showing six nucleotides bonded
together as a single-stranded polymer. Answer the following.
1. Within the polymer of six nucleotides, which sugar carbons are bonded to
phosphate groups? (Do not consider the first nucleotide.)
2. Within a single nucleotide, what number carbon is always attached to the
phosphate group?
3. Which carbon number is always attached to the nitrogenous base?

Nucleotides bond to one another to form a chain or polymer as a result of

condensation reactions forming covalent bonds between the sugar of one
nucleotide and the phosphate group of the next nucleotide. The fact that covalent
bonds hold the chain together is important as covalent bonds are relatively strong
(require a great deal of energy to break) and thus a nucleic acid polymer made of
nucleotides is quite stable.

A1.2.4 - Nitrogenous bases within nucleic acids

A1.2.4 - Bases in each nucleic acid that form the basis of a code
Students should know the names of the nitrogenous bases.

In total, there are five possible nitrogenous bases in RNA and DNA. Four are found
within RNA, and four are found in DNA. Only one of the bases differs in the two types
of polymers, as shown in Table 1.

RNA nitrogenous bases DNA nitrogenous bases

Adenine (A) Adenine (A)

Uracil (U) Thymine (T)

Cytosine (C) Cytosine (C) Make sure you know

the names of the five
Guanine (G) Guanine (G) nitrogenous bases
found in RNA and
DNA, and do not just
A1.2 Table 1 The ve nitrogenous bases found in RNA and DNA
rely on the abbreviated
form of a capital letter.
It may look like some of the nucleotides found in RNA and DNA are identical, for
example because they both contain the base adenine. However, they are not identical
The sequence of
because all the nucleotides found in RNA contain ribose as their pentose sugar, and all nitrogenous bases
the nucleotides in DNA contain deoxyribose. In addition, the base uracil only occurs in DNA, later
in RNA, not DNA, and the base thymine only occurs in DNA, not RNA. Thus, there are transcribed into
eight different nucleotides in total. When drawing nucleotides, it is common practice RNA, forms the basis
of the genetic code.
to put the capitalized first letter of the base inside the rectangle, as used by the IB.

19
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A UNITY AND DIVERSITY Molecules

Challenge yourself
4. Use the geometric symbols required by the IB (see Figure 1) to represent all the
5' end possible separate nucleotides of DNA. Once you have sketched the four for
DNA, do the same for RNA. To remind yourself of the fundamental pentose
A sugar difference between RNA and DNA nucleotides, you might want to put the
letter "R", for ribose, inside the pentose shape of all RNA nucleotides. Then put
"DR", for deoxyribose, inside all of the four DNA nucleotides. Make sure you
end up with eight different nucleotides in total, one containing uracil and one
2
containing thymine.

3 A1.2.5 - The structure of RNA

A1.2.5 - RNA as a polymer formed by condensation of nucleotide monomers
4 Students should be able to draw and recognize diagrams of the structure of single nucleotides
and RNA polymers.

RNA is formed when nucleotides become bonded together in very specific sequences. The
nucleotides are joined together by a condensation reaction between the pentose sugar of
one nucleotide and the phosphate group of the next nucleotide. This reaction releases a water
molecule (which is why this is called a "condensation" reaction). If an RNA molecule contains
322 nucleotides, 321 molecules of water would have been produced during its synthesis, as it
would have required 321 condensation reactions to form.

Challenge yourself
5. How many water molecules would have been produced when the condensation
reactions occurred that produced the 12 nucleotide RNA sequence shown in
Figure 3?

9
i Even though the RNA depiction in Figure 3 has only 12 nucleotides shown, the actual RNA
may have as many as a few thousand nucleotides.

A1.2 Figure 3 Twelve nucleotides bonded to form a very small section of a strand of RNA.
The molecule is recognized readily as RNA because of the presence of uracil and because it is a
single strand. Each adjoining nucleotide has been drawn in a different colour to emphasize the
nucleotide structures. Notice that the chain has an alternating pentose-phosphate backbone, with
10 the nitrogenous bases extending outwards from the backbone.

11

12

3' end

20
 Nucleic acids A1.2

A1.2.6 - The structure of DNA

A1.2.6 - DNA as a double helix made of two antiparallel strands of nucleotides with
two strands linked by hydrogen bonding between complementary base pairs
In diagrams of DNA structure, students should draw the two strands antiparallel, but are not
required to draw the helical shape. Students should show adenine (A) paired with thymine (T),
and guanine (G) paired with cytosine (C). Students are not required to memorize the relative
lengths of the purine and pyrimidine bases, or the numbers of hydrogen bonds.

Cytosine Guanine

Thymine Adenine

RNA is composed of a single chain or strand of nucleotides, while DNA consists of

two chains or strands of nucleotides connected to one another by hydrogen bonds. The nitrogenous
bases adenine
The strands of both DNA and RNA may involve very large numbers of nucleotides.
and thymine are
To visualize DNA, imagine the double-stranded molecule as a ladder (see Figure 4). always paired with
The two sides of the ladder are made up of the phosphate and deoxyribose sugars. The each other in the
rungs of the ladder (what you step on) are made up of the nitrogenous bases. Because double-stranded
the ladder has two sides, there are two bases making up each rung. The two bases DNA molecule.
Likewise, cytosine
making up one rung are said to be complementary to each other. Notice that the base and guanine are
pairs are always adenine (A) bonded to thymine (T) and cytosine (C) bonded to guanine always paired. These
(G). There are no exceptions to this in DNA, and these base pairings are known as the
complementary base pairs. Because the two strands are upside down in comparison phercomple callery
base pairs.
to each other, but parallel, they are said to be antiparallel to each other.

3' A1.2 Figure 4 A small

5' section of a double-
A :: :T- stranded DNA molecule
showing hydrogen bonds
(dotted lines) between
3'
G "' complementary base pairs.
This type of representation
of DNA is known as a "ladder
5' diagram" and does not
direction direction attempt to show the helical
3' 3'
in shape of the molecule.

5'
3'
3'
5'
I Can 6 " 5'

3' Two antiparallel strands of DNA

21
A UNITY AND DIVERSITY Molecules

Always attempt to
view DNA and RNA
Challenge yourself
molecules as chains of
nucleotides. Identify
the first nucleotide with

its own phosphate, T ::: A

sugar and nitrogenous
base and then visually
move to the next, and
so on. In Figure 4 you
would visually start in

the upper left corner

for the left strand, and G
you would start in the
lower right corner for
the right strand.

6. On your own paper and using the figure above as a guide, sketch and label the
geometric shapes as shown to represent this four-nucleotide section of DNA.
7. Add four more nucleotides to each side by adding to the bottom of your sketch
so that you end up with a 12-nucleotide section of antiparallel DNA. Remember
to use complementary base pairs, although you can choose the base sequence.
8. Circle two complete nucleotides of your added nucleotides, one on each side, but do
not circle any of the nucleotides in the corners of the figure. Check to make sure
that your circles include one phosphate group, one deoxyribose sugar and one
nitrogenous base, and that there are no uncircled nucleotides that are incomplete.

A1.2.7 - Distinguishing between DNA and RNA

A1.2.7 - Differences between DNA and RNA
Include the number of strands present, the types of nitrogenous bases and the type of pentose
sugar.
Students should be able to sketch the difference between ribose and deoxyribose. Students
should be familiar with examples of nucleic acids.

DNA and RNA are both linear polymers, consisting of sugars, phosphates and
bases, but there are some important differences between the two molecules. Table 2
summarizes these differences.

DNA RNA
Double-stranded molecule Single-stranded molecule
All nucleotides contain deoxyribose sugar All nucleotides contain ribose sugar
Thymine is one of the four nitrogenous bases Uracil is one of the four nitrogenous bases
Shaped into a double helix Variety of shapes depending on type of RNA
Acts as the permanent genetic code of a cell/organism Does not contain a permanent genetic code, except in RNA viruses

A1.2 Table 2 A comparison of DNA and RNA molecules

22
 Nucleic acids A1.2
Distinguishing between deoxyribose and ribose Practise sketching each
SKILLS of the two molecules
Ribose has a molecular formula of C,H,,O,, whereas deoxyribose has a formula of
shown in Figure 5.
Learn the pattern that
rise one the he gal difre in the olecula chemiyal dorma is that
shows where the difference occurs (see Figure 5). In organic chemistry an -OH group is comes to both
bonded to a carbon is called an alcohol or hydroxyl group. If you remove the oxygen modify for the
single difference
from the hydroxyl group, it simply leaves a hydrogen. This may not look like much, between deoxyribose
but it is the common difference in all nucleotides of RNA versus DNA. and ribose.

HOCH, HOCH,
OH

H
The single "missing"
oxygen in the pentose
OH OH Он] sugar of DNA leads to
the name deoxyribose
deoxyribose ribose within the full name
for DNA (deoxyribose
A1.2 Figure 5 A molecular sketch showing the deoxyribose sugar of DNA compared to the ribose nucleic acid). The
sugar found in RNA molecules. Notice the difference in the lower right corners of the two molecules. full name of RNA is
Ribose has one more oxygen in its structure compared to deoxyribose. ribonucleic acid.

Speci c examples of nucleic acids

All living organisms use DNA as their long-term hereditary storage molecule. DNA
stores genetic information as genes, but for that information to become useful to a cell
there must be other nucleic acids at work. Here are four of the other nucleic acids as
examples.

• Messenger RNA (mRNA) - This is an RNA molecule that is synthesized from

an area of DNA called a gene. In a cell with a nucleus, the mRNA then leaves
the nucleus and represents the genetic information necessary to make a protein.
This is where it gets its name "messenger" RNA.
• Transfer RNA (tRNA) - Special genes of DNA code for tRNA molecules.
When a specific protein is synthesized, specific amino acids must be added to
the amino acid chain in a specific order. The function of tRNA is to transfer the
correct amino acid into a growing chain of amino acids. This is the reason for its
name "transfer" RNA.
• Ribosomal RNA (rRNA) - Again, special genes of DNA code for rRNA
molecules. Along with some previously synthesized proteins, rRNA is used Do not concern
to create an organelle in cells called ribosomes. Cells typically have many yourself at this point
with the details of these
thousands of ribosomes, and they are the cellular location where proteins are
examples of nucleic
synthesized. acid molecules, beyond
• Adenosine triphosphate (ATP) - This is a single-nucleotide nucleic acid. what is summarized
in this section. The
There are many other single-nucleotide nucleic acids in cells, but we are going
function of each of
to use this one as an example. ATP is used in cells as a type of chemical energy. these molecules is
When a muscle contracts, many ATP molecules are used as an energy source explained in much
for the movement. The ultimate purpose of cellular respiration is to convert the greater detail in other

energy contained within food molecules into the energy of ATP. chapters.

23
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A UNITY AND DIVERSITY Molecules

Challenge yourself
The figure below shows a molecular diagram of an ATP molecule. You do not need
to memorize it, but based on what you have read earlier in this chapter you should
be able to look at the diagram and answer the following questions.
9. Why is this molecule called a "triphosphate"?
10. Is the pentose sugar in this molecule ribose or deoxyribose?
11. The "adenosine" portion of the molecule's name comes from the nitrogenous
base bonded to the pentose sugar. What is that nitrogenous base?

NH2

|I

HO •0

OH •0.

OH OH

A1.2.8 - The importance of complementary base

pairing

A1.2.8 - Role of complementary base pairing in allowing genetic information to be

replicated and expressed
Students should understand that complementarity is based on hydrogen bonding.

As you recall, adenine and thymine are complementary to each other in DNA, and
cytosine and guanine are complementary as well. This complementarity is based on
hydrogen bonding. Adenine and thymine only form hydrogen bonds with each other;
adenine does not form hydrogen bonds with any other DNA nucleotide. The same is
true for cytosine and guanine.

24
 Nucleic acids A1.2
hydrogen

• nitrogen
• oxygen
• carbon

cytosine guanine thymine adenine

Hydrogen bonding (shown in dotted red lines) between the complementary base pairs within DNA. It
is this hydrogen bonding that holds the two antiparallel strands together and ultimately results in the
double helix shape.

Complementary base pairing is important in DNA replication. Imagine that an area of

DNA has been unzipped (opened up into two single strands). If free-floating individual
nucleotides in solution begin pairing with the unmatched nucleotides, an exact copy
of the original molecule can be made. In fact, if both sides of the original DNA are used
as a template, then two molecules of DNA can be synthesized, each a duplicate of the
original. In a simplified form, this is how DNA replication occurs.

A1.2.9 - Storage of genetic information

A1.2.9 - Diversity of possible DNA base sequences and the limitless capacity of DNA
for storing information
Explain that diversity by any length of DNA molecule and any base sequence is possible.
Emphasize the enormous capacity of DNA for storing data with great economy.

DNA stores genetic information in its sequence of nitrogenous bases. Every three bases
represents a meaningful piece of information called a triplet or, more specifically, a
triplet codon. Many triplets within DNA code for one of the 20 amino acids. There are
four different DNA nucleotides that can be arranged as sequenced triplets. So, what
are the odds of DNA containing any one triplet in any one gene location? Consider
the odds of having G-G-G in one triplet area of DNA. If it was by random chance
(although it is not) the odds would be:

1*4 4=64
1
Why? Because there is a one in four chance of the nitrogenous base being guanine, and
it occurs in our example three times.

This computation also means that there are 64 combinations of nucleotides within the
triplet code system. All of those 64 combinations are used in the genetic code for some
purpose, most of them coding for amino acids.

25
 A UNITY AND DIVERSITY Molecules

i
Researchers are
Think about all the ways that the four nitrogenous bases of DNA can be grouped.
working on ways to If DNA was a short molecule (say around 1,000 nucleotides), the number of groupings
store data (text les, would be large, but still not unlimited. Now consider that the length of DNA (the
photos, books, maps)
number of nucleotides in one strand) is only limited by the amount that will fit
within arti cially
created DNA efficiently into a cell. The shortest DNA molecule in the human genome is about
molecules. DNA stores 50 million base pairs, and the longest about 260 million base pairs.
information using the
very ef cient code As you can see, the likelihood that two DNA molecules are identical as a result of
of four nitrogenous
random chance approaches zero. DNA can contain a nearly limitless amount of
bases, compared to
the less ef cient 0 and genetic information.
1 binary code used by
computers.

A1.2.10 - Genetic uniqueness

How can polymerization
result in emergent
properties? A1.2.10 - Conservation of the genetic code across all life forms as evidence of
universal common ancestry
Students are not required to memorize any specific examples.

Imagine a section of DNA that contains the triplet code C-G-A. If that triplet code is
Identical twins develop
when a single fertilized
egg or early embryo
i used to synthesize a protein, the amino acid that will be produced will be alanine. If
the triplet code is A-G-A, the amino acid is serine. A chart listing the triplet codes can
splits into two portions.
provide this information.
Each grows to become
a separate person and
It does not matter whether the organism is a species of fungus, an oak tree, or a human
shares exactly the same
DNA sequences.
being. All living organisms use the same genetic code. The genetic code is therefore
said to be universal.

So why are organisms different from each other? The answer to that is the DNA base
What makes RNA more
likely to have been the
sequences are different even though the code to read the sequences is the same. Your
first genetic material, best friend, although not directly related to you, is related to you by evolution. The two
rather than DNA? of you share more than 99% of the same gene sequences. If it was 100%, you would not
be the unique and different people you are.

A conserved genetic code

Why has the genetic code remained unchanged? The
answer to this question lies in the process of evolution.
The evolution of living organisms has been occurring
for over 3.5 billion years. If you could go back in
time far enough you would probably not see any
organisms that you recognize today, although some
of the organisms you would see will be the ancestors
of today's organisms. If you were to keep moving back
through time, the organisms would become even less
familiar, and eventually they would be nothing more
than single-celled organisms living in water.

Bacteria and protists were some of the first organisms on Earth

to evolve, and thus hold the origin of the genetic code used
by all organisms today. Humans and other life forms still have
genes in common with these evolutionary pioneers.

26
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 Nucleic acids A1.2
These single-celled organisms are the ancestors of all life on Earth today. This is also
postulated to be the time period in which the biochemistry of DNA and RNA evolved.
All life forms from that point on used DNA to store their genetic information, and RNA
to transfer that information to the order of amino acids in their proteins. Evolution 5' end
changes the DNA sequences slowly, but it always has continued to use the same
mechanisms of genetic coding. A
Nature of Science
The theory of evolution by natural selection as proposed by Charles
Darwin and independently by Alfred Wallace was based primarily on their 2
observations of physical traits. It appeared to them that organisms developed
adaptations to fit different ecological niches in the area that they lived in. In
1859, when Darwin published his famous book On the Origin of Species, there
was absolutely no knowledge of DNA or the molecular basis of heredity and
3
evolution. Scientific ideas that originate in one form can be corroborated
by later scientific work if the ideas are sound. Today there is a mountain of
U
evidence supporting evolutionary principles, including a vast amount of 4
information from molecular genetics.

5
HL

A1.2.11 - Directionality of RNA and DNA strands

A1.2.11 - Directionality of RNA and DNA

Include 5' to 3' linkages in the sugar-phosphate backbone and their significance for
replication, transcription and translation.
7
The 5' and 3' designations refer to the fifth and third carbon atoms in the ribose and
deoxyribose sugars (see Figures 5 and 6).

In a DNA molecule there are two strands that run antiparallel to each other. This means
that if you compare the sides of DNA, one strand will run 5'to 3' and the other will run 3'
to 5'. This does not mean the direction in which they were synthesized is different. Both
9
strands of DNA are synthesized starting with the 5' nucleotide and working towards the
3' end.

DNA does not have a single 5' end or 3' end. DNA is composed of two strands
and each strand has a 5' and 3' end. 10

11
A1.2 Figure 6 This is the same very small section of RNA you studied in Figure 3. Because each
nucleotide has one phosphate, one sugar and one nitrogenous base, there are 12 of each of these
subunits. Any single strand of DNA or RNA will have an unbound phosphate group at one end (the
upper left corner). This end is identi ed as the 5' (5 prime) end of the strand. All the other phosphate
groups are bonded to two sugars, linking adjacent nucleotides. The opposite end of the strand 12 G
terminates with deoxyribose sugar with no additional phosphate groups. This end is called the 3' (3
prime) end of the strand. 3' end

27
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 A UNTY AND DIVERSITY Molecules

Challenge yourself
12. Since the two strands of DNA are antiparallel to each other, you only need to
know one end of one strand in order to extrapolate the other three ends.

3'
Y
Each horizontal line shown above represents a strand of DNA of a double-
stranded molecule. Notice that only the 3' end of one strand has been labelled.
Using 5' and 3', label each of the ends currently labelled X, Y and Z.

The importance of directionality

When RNA or DNA is formed, one nucleotide at a time is added to the molecule.
The nucleotide is not added at a random spot: it is added as the next nucleotide
in a growing chain. As all nucleotides have a phosphate group, pentose sugar and
nitrogenous base, you can trace this formation by looking for the first nucleotide in the
sequence. That first nucleotide will always be the 5' end of the strand

This is important when a new nucleic acid strand is formed. When DNA replicates, the
two strands separate from each other in a particular area, and each separated strand
acts as a template for a new strand to be formed. A new strand will always begin with
the 5'-end nucleotide first.

DNA and RNA molecules are both integral to the process of protein synthesis. The
first stage of protein synthesis is called transcription. This occurs when a gene of
DNA (one of the two DNA strands) is opened and an RNA molecule is synthesized
using complementary base pairing. The transcription process synthesizes the 5'
end of the RNA first. The resulting RNA is called mRNA, and represents the genetic
Any new nucleic information of one gene. The mRNA then pairs with an organelle in the cell called a
acid strand being ribosome. Another RNA called tRNA, bonded to a specific amino acid, now pairs
formed (DNA or (by complementary base pairing) to triplets of the mRNA. This process is called
RNA) is always translation. Translation is accomplished in a sequence starting nearest to the 5' end
formed by starting
at its 5' end and of the mRNA molecule. These molecular processes will be difficult to understand
continuing until the completely and visualize until you study Chapter D1.1 on DNA replication and
nal nucleotide is Chapter D1.2 on protein synthesis. For now, visualize nucleic acids as having a
bonded at the 3' directionality (5' and 3' ends), and remember that the directionality is important to
end.
their structure and function in DNA replication and RNA synthesis.

A1.2.12 - Purine-to-pyrimidine bonding

A1.2.12 - Purine-to-pyrimidine bonding as a component of DNA helix stability
Adenine thymine (A-T) and cytosine guanine (C-G) pairs have equal length, so the DNA
helix has the same three-dimensional structure, regardless of the base sequence.

The nitrogenous bases of DNA are grouped into pyrimidines and purines, as shown
in Table 3. Pyrimidines are smaller as they contain a single-ringed structure, whereas
purines are larger as they contain a double-ring structure.

28
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 Nucleic acids A1.2
Purines Pyrimidines
(double ring size) (single ring size)
Adenine (A) Thymine (T)
Guanine (G) Cytosine (C)

A1.2 Table 3 Types of nucleotides found in DNA

When bonding the two strands of DNA together to make the double helix, a purine is
always bonded to a pyrimidine. This results in the two strands of DNA being a consistent
distance from each other (with three rings in total), leading to an amazing and stable
double helix shape as the two strands wind around each other in three dimensions.

HWH This gure shows

Adenine (A) complementary base pairing
and nitrogenous base
H structures within a small
H portion of DNA. You do
not have to memorize the
О=Р-0 H nitrogenous base structures
for the IB. Notice the double-
N-H ring structures of adenine
N=C, and guanine (purines) and
H-C-HO. the single-ring structures

H-CI С-н
HHH
of thymine and cytosine
(pyrimidines).
C-C H
Thymine (T)
H

HIN-H H
0=р C-c
//
H

Сно -N
HH
H
/С-н
с-с
i
H Cytosine (C)
You learned that

/
OH-C
.C
complementary base
pairing requires A-T
and C-G. As you can

С-с
ỚH
see, in each case one
is a purine and the
H other a pyrimidine.
HIN-H But, why not G-T and
A-C? Even though that
N
H с-н pairing would bond a
purine to a pyrimidine,
hydrogen bonding
C between the pairings
Guanine (G) P=0 cannot occur and thus
it does not occur in
nature.

29
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A UNTY AND DIVERSITY Molecules

A1.2.13 - Efficient packaging of DNA molecules

A1.2.13 - Structure of a nucleosome
Limit to a DNA molecule wrapped around a core of eight histone proteins held together by an
additional histone protein attached to linker DNA.
Application of skills: Students are required to use molecular visualization software to study
the association between the proteins and DNA within a nucleosome.

A1.2 Figure 7 One

chromosome from a cell's
DNA
nucleus expanded to show
the coiling and structure of base pair
nucleosomes. nucleus

chromosome

cell
histone —
proteins

nucleosomes

DNA is a very, very long molecule. Some DNA molecules in human cells are

i
Biologists often
describe DNA approximately 2 m in length. In order to fit the very long molecules of DNA inside
organized into the nucleus of a cell, a very efficient "packaging" solution has evolved (see Figure 7).
nucleosomes as "beads Within the nucleus there are proteins called histones. First, DNA wraps itself around
on a string". In this
eight of these histone proteins, and then an additional histone helps hold the structure
analogy, the DNA (the
string) is wrapped
together. This occurs in many adjoining areas of DNA. Each resulting structure is
around the histones called a nucleosome (see Figure 8). The DNA that extends from one nucleosome to
(the beads), rather than the next is called linker DNA. The multitude of nucleosomes then stack
running through them
up in an organized pattern and begin coiling around other proteins in a very
as in an actual beads.
condensed shape. The overall "packaged" shape is a chromosome. A human cell
contains 46 chromosomes.

You can find videos and other molecular visualization aids online to view the use of histone
SKILLS proteins to form nucleosomes and the formation of chromosomes.

30
 Nucleic acids A1.2
eight histones make linker DNA
up the nucleosome going to
core next
nucleosome

histone
maintaining the
shape of the
nucleosome
DNA wraps twice around linker DNA extending from
the eight histones of the
the previous nucleosome
nucleosome core

A
A1.2 Figure 8 A nucleosome showing the DNA wrapped around eight histone proteins with one
additional histone helping to keep the structure intact. Linker DNA is found between adjoining
nucleosomes. Look back at Figure 7 to see how nucleosomes organize into a chromosome.

A1.2.14 - The Hershey-Chase experiment

A1.2.14 - Evidence from the Hershey-Chase experiment for DNA as the genetic
material
Students should understand how the results of the experiment support the conclusion that
DNA is the genetic material.
NOS: Students should appreciate that technological developments can open up new
possibilities for experiments. When radioisotopes were made available to scientists as
research tools, the Hershey-Chase experiment became possible

Before the middle decades of the 20th century, biologists were unsure of the genetic
Sometimes it is dif cult
material of living organisms. Primarily, they debated whether genetics was based ТОК for scientists to let go of
on nucleic acids or proteins. Because DNA was composed of only four types of long-held beliefs. The
nucleotides, and proteins were composed of 20 types of amino acids, it made sense to beliefs become ingrained
as part of their core
many that proteins could better provide the complex genetic variety found in living
knowledge, and few
organisms. even think to challenge
that knowledge. How
In 1951 and 1952, two researchers, Alfred Hershey and Martha Chase, working at Cold do our expectations
Spring Harbor, NY, carried out experiments that helped confirm DNA as the genetic and assumptions have
material. The experiment used a bacteriophage and the bacterium Escherichia coli. A an impact on how we
perceive things?
bacteriophage is a virus that infects bacteria, and is composed of a protein outer coat
and an inner core of DNA. When a bacteriophage infects a cell, the virus takes over the
metabolism of the cell, resulting in multiple viruses of that type being formed using
molecules such as nucleotides in their synthesis.

Hershey and Chase made use of radioisotopes in their experiment in a process called
radioactive isotope labelling. Radioisotopes are radioactive forms of elements that
can be detected within molecules. The particles released during their decay allow the
specific radioisotope used to be detected. The researchers grew bacteriophage viruses

31
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A UNTY AND DIVERSITY Molecules

in two different types of culture. One culture included radioactive phosphorus 32.
The viruses produced in this culture had DNA inside their viral core labelled with
the detectable phosphorus 32. Another culture included a radioactive form of sulfur
known as sulfur 35. This detectable radioisotope was present in the protein outer coat
of the viruses produced. DNA does not include sulfur (because nucleotides do not
contain any sulfur atoms). The radioactive sulfur was only detectable in the protein
shell of the virus, because two of the 20 possible amino acids that can be present in
protein contain sulfur.

The two types of bacteriophages labelled with radioisotopes were each allowed to
infect the bacterium E. coli. As Figure 9 shows, the E. coli infected with the phosphorus
32-labelled bacteriophage had radioactivity detected inside the cells, a location
indicating DNA. However, the E. coli infected with the sulfur 35-labelled bacteriophage
had no radioactivity inside the cell. Because DNA contains phosphorus and not sulfur,
this allowed Hershey and Chase to conclude that DNA, not protein, was the genetic
material.

Once the results of the Hershey-Chase experiment were published, further research
It is important for
researchers to publish involving genetics centred primarily on DNA was possible, and collectively that body
the details and findings of work provides conclusive evidence that DNA is the genetic material.
of their experimental
work. This allows other
scientists all over the
world to learn and
build upon previous
work in future research
projects.
bacteriophage with phage infects radioactivity inside
phosphorus 32 in DNA bacterium bacterium
The Hershey-Chase
experiment is
sometimes referred
to as the "blender
experiment" because
the experimental
process involved using
a kitchen-type blender. bacteriophage with phage infects no radioactivity inside
The blender sheared sulfur 35 in protein coat bacterium bacterium
the viral coatings
containing the sulfur
radioisotope away A1.2 Figure 9 A summary of the Hershey-Chase experiment. Radioactivity was detectable inside
from the living bacterial cells after radioactive isotopes of phosphorus had been used when growing E. coli cultures. These
cells containing radioactive isotopes were used within the nucleotides when E. coli cell division occurred and DNA was
the phosphorus
replicated. Recall that phosphorus is a component of nucleotides within phosphate groups.
radioisotope.

Nature of Science
It is not very often that "eureka" moments occur in science. More often
scientific advances move along slowly, with one discovery providing
information that leads to another. Such was the case with the Hershey-
Chase experiments. Their work was made possible by earlier research using
radioactive isotopes to trace the pathway of different types of molecules. The
Hershey-Chase work showing DNA is the genetic material was not the result
of a single experiment but a series of experiments, during which techniques
were refined as they worked through the problem one step at a time.

32
 Nucleic acids A1.2

A1.2.15 - Chargaff's rule

A1.2.15 - Chargaff's data on the relative amounts of pyrimidine and purine bases
across diverse life forms

NOS: Students should understand how the "problem of induction" is addressed by the
"certainty of falsification". In this case, Chargaff's data falsified the tetranucleotide hypothesis
that there was a repeating sequence of the four bases in DNA.

rod holding
paper

chromatography
paper
beaker
pencil line -
the samples
started here
- solvent

at the start after the solvent has

soaked up the paper

Erwin Chargaff's experimental work determining the nitrogenous base ratios within DNA involved the
technique shown in this gure: paper chromatography. A mixture of substances is embedded into

soon. The phen ver The ore after are on ones of ted be antes a componen .
travels a different distance based on its molecular size and charge.

As mentioned earlier, scientists in the early part of the 1900s worked under the
assumption that protein was responsible for genetic traits. Research showed that there
were both DNA and proteins in the nucleus of a cell. The hypothesis was that DNA
existed as a tetranucleotide molecule, in other words, in repeating set units of the four
nucleotides, and was there to help give structure to chromosomes.

In the late 1940s a researcher named Erwin Chargaff developed a research technique
designed to show the proportions of nitrogenous base types found in various sources
of DNA. His separation and identification technique involved paper chromatography.
Some of the results of his studies are shown in Table 4.

DNA source Adenine Thymine Guanine Cytosine

Calf thymus 1.7 1.6 1.2 1.0
Beef spleen 1.6 1.5 1.3 1.0
Yeast 1.8 1.9 1.0 1.0
Tubercle bacillus 1.1 1.0 2.6 2.4

A1.2 Table 4 A summary of some of the data from Chargaff's research. Look for approximate 1:1
proportions, reading across the table for each of the four sources of DNA

33
fi
 A UNITY AND DIVERSITY Molecules

Start by looking at the results for the DNA Chargaff extracted from the thymus gland
of a calf. As you can see, there is almost the same ratio of adenine to thymine, and
also the same ratio of guanine to cytosine. Very similar ratios exist for the other three
biological sources of DNA shown.

James Watson and Over time, this and similar data became known as Chargaff's rule: DNA contains
Francis Crick made the same number of adenine as thymine nucleotides, as well as the same number of
use of information guanine and cytosine nucleotides.
provided by several
other research teams
when they proposed
Nature of Science
and built the rst
Why do you think it is that the ratios of A-T and C-G were not a perfect 1:1 in
accurate model of
DNA in 1953. X-ray Chargaff's results? Depending on the experimental methodology used, science
crystallography work often does not give perfect results. This is frequently because of experimental
by Rosalind Franklin error. Some of that error could be human error, and sometimes it is the best
showed DNA to be
data that the technique can produce. It does not mean that the data is useless.
a double helix. Erwin
Chargaff's work showed A large data set can minimize some of the error, and statistics can show how
the complementary significant the errors are.
pairing of the
nitrogenous bases.

The importance of Chargaff's rule

The data from Chargaff's work not only showed that the proportion of adenine to
thymine, and guanine to cytosine, is equal, it also showed that the tetranucleotide
theory is false. The tetranucleotide theory, if correct, would have resulted in the
proportion of all of the nitrogenous bases being equal. In other words, the same
quantities of A, T, C and G. The data did not show equal proportions of all four bases,
and thus the tetranucleotide idea was falsified.

This led to a whole new set of ideas as to what the genetic code could be. Researchers
began to consider the sequence of nucleotides in DNA as highly variable and the
possibilities of DNA containing the genetic code. We now know the proteins in the
nucleus of the cell were primarily histone proteins helping to form nucleosomes.

Nature of Science
The process of science always struggles with the conclusions that can be reached
from various data sets. The "problem of induction" is evidenced by assuming
something is always true because one or more data sets seems to lead to that
conclusion. In actuality, the process of science is often better served by asking
questions that lead to falsifications. This is what Erwin Chargaff did when he
falsified the idea that DNA was organized into tetranucleotides.

HL end

34
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 Nucleic acids A1.2

Guiding Question revisited

How does the structure of nucleic acids allow hereditary information to be
stored?

In this chapter we have described how RNA and DNA are structured:

• each is composed of subunits called nucleotides

• nucleotides exist in eight types, four types in RNA and four types in DNA
• each nucleotide contains one of five possible nitrogenous base, adenine,
thymine, cytosine, guanine and uracil
• in DNA, the two strands are held together by complementary base pairing
between the nitrogenous bases
• the sequence of the nucleotides in sections of DNA called genes allows long-
term storage of the genetic code
• RNA molecules are complementary copies of genes of DNA transcribed by
using RNA nucleotides.

Guiding Question revisited

How does the structure of DNA facilitate accurate replication?

In this chapter we have described how:

• DNA exists as a double-stranded molecule

• DNA makes copies of itself
• this unwinding allows the nitrogenous bases to make new complementary
pairings using the exposed nitrogenous bases as a template
• the pairings are adenine with thymine, and cytosine with guanine
• two DNA molecules are created from one during DNA replication, although
neither is completely "new"
• HL nitrogenous base sizes (a purine with a pyrimidine) and hydrogen
bonding ensure accuracy when new base pairs are formed.

Exercises
Q1. State how many nucleotide types exist within the structures of DNA and
RNA.

Q2. State the structural similarity of the two nitrogenous bases (adenine and
guanine) used to classify them as purines.

35
A UNITY AND DIVERSITY Molecules

Q3. Suggest a reason why researchers often give DNA information:

(a) as the sequence of nitrogenous bases without indicating the presence
of the phosphate group and sugar component of each nucleotide (for
example 5'ATTCCGTGTACGT3')
(b) from one strand of DNA only.

Q4. You are visualizing a single sequence of nitrogenous bases and you see
multiple uracil bases. What does that tell you about the molecule?

Q5. Which of these is not a nucleic acid?

A DNA B ATP D RNA
Q6. A measurement of a sample of DNA showed that 22% of the nitrogenous
bases were cytosine. Calculate the expected percentage of the following
nitrogenous bases:
(a) guanine
(b) adenine
(c) thymine.

HL/
Q7. Even though cytosine is a pyrimidine and adenine is a purine, they are not
complementary to each other. State what prevents these two bases from
being complementary to each other within DNA.

Q8. In the experimental work by Hershey and Chase, why was the presence of
radioactive phosphorus correlated with DNA and not protein?

Q9. Which statement best describes a single chromosome?

A A length of DNA coiled around eight histone proteins with an additional
histone.
B A length of DNA coiled around many groupings of eight histones each
having one additional histone.
C Protein structures found within the nucleus of a cell.
D DNA structures found within the nucleus of a cell.
HL end

36
 Practice questions A1
A1 Practice questions
1. Describe the importance of water to living organisms.
(Total 5 marks)

2. Draw a labelled diagram showing the structure of three water molecules and
how they interact.
(Total 4 marks)

Global warming has changed both the thickness and surface area of sea ice of
the Arctic Ocean as well as the Southern Ocean that surrounds Antarctica.
Sea ice is highly sensitive to changes in temperature.

Scientists have calculated a long-term mean for the surface area of sea ice in
the Arctic and in the Southern Ocean around Antarctica. This mean value
is used as a reference to examine changes in ice extent. The graph shows the
variations from this mean (zero line) over a period of time.
4

key:
Arctic
--- trend line
— variations
standard deviations

Antarctica
_ trend line
variations in surface area of sea ice /

variations

1978 81 84 87 90 93 9699 02 05 08 2011

year

(a) State the trend in the surface area of sea ice in the Southern Ocean
around Antarctica. (1)
(b) Distinguish between changes in the surface area of sea ice in the Arctic
and Antarctica. (2)
(c) Discuss the data as evidence of global warming. (3)
(Total 6 marks)

4. Draw a labelled diagram of a section of DNA showing four nucleotides.

(Total 5 marks)

HL Outline the structure and functions of nucleosomes.

(Total 4 marks)

37