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12. Energy & Respiration ⬇

CONTENTS
12.1 Energy
12.1.1 Energy

12.1.2 ATP

12.1.3 Energy Values of Respiratory Substrates

12.1.4 Respiratory Quotient (RQ)

12.1.5 Investigating RQs

12.2 Respiration
12.2.1 Structure & Function of Mitochondria

12.2.2 The Four Stages in Aerobic Respiration

12.2.3 Aerobic Respiration: Glycolysis

12.2.4 Aerobic Respiration: The Link Reaction

12.2.5 Aerobic Respiration: The Krebs Cycle

12.2.6 Aerobic Respiration: Role of NAD & FAD

12.2.7 Aerobic Respiration: Oxidative Phosphorylation

12.2.8 Anaerobic Respiration

12.2.9 Energy Yield: Aerobic & Anaerobic Respiration

12.2.10 Anaerobic Adaptation of Rice

12.2.11 Aerobic Respiration: Effect of Temperature & Substrate Concentration

12.1 ENERGY

12.1.1 ENERGY

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12. Energy & Respiration ⬇

The Need for Energy

Living organisms are composed of cells, and within each cell, many activities and
processes are constantly being carried out to maintain life

Work in a living organism requires energy and usable carbon compounds

Essential work within organisms table

The source of energy & materials

For nearly all organisms the sun is the primary source of energy
The reactions of photosynthesis store energy in organic molecules
Light energy from the sun is transformed into chemical potential energy in the
synthesis of carbohydrates

The carbohydrates formed are then used in the synthesis of ATP (from their
breakdown) or are combined and modified to form all the usable organic molecules
that are essential for all metabolic processes within the plant

Photosynthesis is carried out by the first organism in a food chain, such as plants and
some other small organisms

Respiration in all living cells releases energy from the breakdown of organic molecules

Respiration involves the transfer of chemical potential energy from nutrient molecules
(such as carbohydrates, fats and proteins) into a usable energy form (through the synthesis
of ATP) that can be used for work within an organism

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12. Energy & Respiration ⬇

Glucose equations
glucose + oxygen → carbon dioxide + water + energy

C6H1206 + 6 O2 → 6 CO2 + 6 H20 + 2870kJ

Autotrophs are organisms that are able to synthesise their own usable carbon
compounds from carbon dioxide in the atmosphere through photosynthesis

Heterotrophs don’t have this ability. They require a supply of pre-made usable carbon
compounds which they get from their food

Exam Tip

According to the laws of thermodynamics, energy cannot be created or

destroyed; it is transformed from one form into another. Be careful not to
say that energy is “created” when talking about photosynthesis and
respiration.
You may also be expected to name examples of energy-requiring reactions in
organisms:
• The sodium-potassium pump that is found on many cell membranes is a
great example of active transport. Three sodium ions are taken out of the cell
while two potassium ions are taken in, both against their respective
concentration gradients
• The movement and contraction of muscles also requires substantial
amounts of energy

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12. Energy & Respiration ⬇

12.1.2 ATP

ATP: Universal Energy Currency

Energy released during the reactions of respiration is transferred to the molecule adenosine
triphosphate (ATP)

ATP is a small and soluble molecule that provides a short-term store of chemical energy
that cells can use to do work

It is vital in linking energy-requiring and energy-yielding reactions

ATP is described as a universal energy currency

Universal: It is used in all organisms

Currency: Like money, it can be used for different purposes (reactions) and is reused
countless times

The use of ATP as an ‘energy-currency’ is beneficial for many reasons:

The hydrolysis of ATP can be carried out quickly and easily wherever energy is
required within the cell by the action of just one enzyme, ATPase

A useful (not too small, not too large) quantity of energy is released from the
hydrolysis of one ATP molecule – this is beneficial as it reduces waste but also gives
the cell control over what processes occur

ATP is relatively stable at cellular pH levels

Structure of ATP
ATP is a phosphorylated nucleotide

It is made up of:
Ribose sugar

Adenine base

Three phosphate groups

Hydrolysis of ATP
When ATP is hydrolysed (broken down), ADP and phosphate are produced

As ADP forms free energy is released that can be used for processes within a cell eg. DNA
synthesis

Removal of one phosphate group from ATP releases 30.8 kJ mol -1 of energy, forming
ADP

Removal of a second phosphate group from ADP also releases 30.8 kJ mol-1 of energy,
forming AMP

Removal of the third and final phosphate group from AMP releases 14.2 kJ mol-1 of
energy, forming adenosine

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12. Energy & Respiration ⬇

Features of ATP table

Exam Tip

Be careful not to use the terms energy and ATP interchangeably. Energy is
the capacity or power to do work. ATP is a molecule which stores (chemical
potential) energy and carries it to places in the cell that need energy to do
work.
For example, saying that “energy is used in muscles” in the exam won’t get
you marks for describing how the muscles work as it is too vague an answer.

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12. Energy & Respiration ⬇

ATP Synthesis

On average humans use more than 50 kg of ATP in a day but only have a maximum of ~
200g of ATP in their body at any given time

Organisms cannot build up large stores of ATP and it rarely passes through the cell
surface membrane

This means the cells must make ATP as and when they need it

ATP is formed when ADP is combined with an inorganic phosphate (Pi) group
This is an energy-requiring reaction

Water is released as a waste product (therefore ATP synthesis is a condensation

reaction)

Types of ATP synthesis

ATP is made during the reactions of respiration and photosynthesis
All of an animal’s ATP comes from respiration

ATP can be made in two different ways:

Substrate-linked phosphorylation

Chemiosmosis

Substrate-linked phosphorylation
ATP is formed by transferring a phosphate directly from a substrate molecule to ADP

ADP + Pi —> ATP

The energy required for the reaction is provided directly by another chemical reaction

This type of ATP synthesis occurs in the cell cytoplasm and in the matrix of the mitochondria

It only accounts for a small amount of the ATP synthesised during aerobic respiration
~ 4 / 6 ATP per glucose molecule

This type of ATP synthesis takes place in glycolysis

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12. Energy & Respiration ⬇

Chemiosmosis
This specific type of ATP synthesis involves a proton (hydrogen ion) gradient across a
membrane

It takes place across the inner membrane of the mitochondria and the thylakoid membrane
of chloroplasts

An electron transport chain helps to establish the proton concentration gradient

High energy electrons move from carrier to carrier releasing energy that is used to
pump protons (up a concentration gradient) across the inner membrane into the
intermembrane space

Protons are pumped from a low concentration in the mitochondrial matrix to a high
concentration in the intermembrane space

The protons then move down the concentration gradient into the matrix which releases
energy

The protons move through the ATP synthase complex which uses the released energy to
drive the phosphorylation of ATP

Oxygen acts as the final electron and proton acceptor to form water

Most of the ATP made during respiration is synthesised via chemiosmosis

~ 32 / 34 ATP per glucose molecule

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12. Energy & Respiration ⬇

ATP synthesis table

Exam Tip

You may be asked to identify which type of ATP synthesis is occurring at

different stages of respiration and photosynthesis. Remember that
chemiosmosis involves a proton gradient that has been created by an
electron transport chain and it takes place across an inner membrane.

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12. Energy & Respiration ⬇

12.1.3 ENERGY VALUES OF RESPIRATORY SUBSTRATES

Energy Values of Respiratory Substrates

Glucose is the main respiratory substrate for aerobic respiration in most cells

When the supply of glucose in a cell has been used up a cell may continue respiration using
other substrates

These may be:

Other carbohydrates

Lipids

Proteins

Amino acids from proteins are only respired aerobically when all other substrates have been
used up
This is because they often have essential functions elsewhere in the cell

Amino acids are required to make proteins which have structural (eg. in the
cytoskeleton) and functional (eg. enzymatic) roles

When these different substrates are broken down in respiration, they release different
amounts of energy

Respiratory substrate table

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12. Energy & Respiration ⬇

Explaining the differences in energy values

Lipids have the highest energy value (39.4 kJ g-1) followed by proteins (17.0 kJ g-1) and then

carbohydrates (15.8 kJ g-1)

The differences in the energy values of substrates can be explained by their molecular
composition
Specifically how many hydrogen atoms become available when the substrate
molecules are broken down

During respiration hydrogen atoms play a vital role:

The substrate molecules are broken down and the hydrogen atoms become available

Hydrogen carrier molecules called NAD and FAD pick them up (become reduced)
and transfer them to the inner mitochondrial membrane

Reduced NAD and FAD release the hydrogen atoms which split into protons and
electrons

The protons are pumped across the inner mitochondrial membrane into the
intermembrane space – forming a proton / chemiosmotic gradient

This proton gradient is used in chemiosmosis to produce ATP

After the protons have flowed back into the matrix of the mitochondria via ATP
synthase they are oxidised to form water

This means that a molecule with a higher hydrogen content will result in a greater
proton gradient across the mitochondrial membrane which allows for the formation of
more ATP via chemiosmosis

Fatty acids in lipids are made up of long hydrocarbon chains with lots of hydrogen atoms.
These hydrogen atoms are released when the lipid is broken down

Exam Tip

You may be expected to explain why different respiratory substrates have

different energy values. Here’s an example question:
Explain why carbohydrates, lipids and proteins have different relative energy
values as substrates in respiration in aerobic conditions. (6 marks)

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12. Energy & Respiration ⬇

12.1.4 RESPIRATORY QUOTIENT (RQ)

Respiratory Quotient (RQ)

The respiratory quotient (RQ) is: the ratio of carbon dioxide molecules produced to oxygen
molecules taken in during respiration

RQ = CO2 / O2

RQ values of different respiratory substrates

Carbohydrates, lipids and proteins have different typical RQ values

This is because of the number of carbon-hydrogen bonds differs in each type of biological
molecule
More carbon-hydrogen bonds means that more hydrogen atoms can be used to create
a proton gradient

More hydrogens means that more ATP molecules can be produced

More oxygen is therefore required to breakdown the molecule (in the last step of
oxidative phosphorylation to form water)

When glucose is aerobically respired equal amounts of carbon dioxide are produced to
oxygen taken in, meaning it has an RQ value of 1

Glucose RQ
C6H1206 + 6O2 → 6CO2 + 6H2O

RQ table

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12. Energy & Respiration ⬇

Exam Tip

Some questions may ask you to suggest what substrate is being respired
during an experiment based on the RQ value – so make yourself familiar with
the values in the table.

Calculating RQs

The respiratory quotient is calculated from respiration equations

It involves comparing the ratios of carbon dioxide given out to oxygen taken in

The formula for this is:

If you know the molecular formula of the substrate being aerobically respired then you can
create a balanced equation to calculate the RQ value

In a balanced equation the number before the chemical formula can be taken as the
number of molecules/moles of that compound
This is because the same number of molecules of any gas take up the same volume
eg. 12 molecules of carbon dioxide take up the same volume as 12 molecules of
oxygen

Glucose has a simple 1:1 ratio and RQ value of 1 but other substrates have more complex
ratios leading to different RQ values

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12. Energy & Respiration ⬇

Worked example: RQ for a lipid

Linoleic acid (fatty acid found in nuts) has the molecular formula C18H32O2

Step 1: Create respiration equation

C18H32O2 + O2 → CO2 + H2O

Step 2: Balance the equation

C x 18 C x 1

H x 32 H x 2

Ox4 Ox3

Step 3: Create the full equation

C18H32O2 + 25O2 → 18CO2 + 16H2O

Step 3: Use RQ formula

CO2 / O2 = RQ

18 / 25 = 0.72

Calculating the RQ for anaerobic respiration

Anaerobic respiration is respiration that takes place without oxygen but does produce a
small amount of ATP

Depending on the organism anaerobic respiration in cells can be done via lactate or ethanol
fermentation
Mammalian muscle cells use lactate fermentation

Plant tissue cells and yeast use ethanol fermentation

The RQ cannot be calculated for anaerobic respiration in muscle cells because no oxygen is
used and no carbon dioxide is produced during lactate fermentation

For yeast cells the RQ tends towards infinity as no oxygen is used while carbon dioxide
is still being produced

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12. Energy & Respiration ⬇

Worked example: RQ for Anaerobic Respiration

Ethanol fermentation in lettuce roots

glucose → ethanol + carbon dioxide + energy

Step 1: Create the respiration equation

C6H12O6 → C2H5OH + CO2 + energy

Step 2: Balance the equation

C6H12O6 → 2C2H5OH + 2CO2 + energy

Step 3: Calculate the RQ value

CO2 / O2 = RQ

2 / 0 = ∞ Infinity

Exam Tip

Make sure the respiration equation you are working with is fully balanced
before you start doing any calculations to find out the RQ value.

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12. Energy & Respiration ⬇

12.1.5 INVESTIGATING RQS

Investigating RQs

Respirometers are used to measure and investigate the rate of oxygen consumption
during respiration in organisms

They can also be used to calculate respiratory quotients

The experiments usually involve organisms such as seeds or invertebrates

Equation for calculating change in gas volume

The volume of oxygen consumed (cm3 min-1) can be worked out using the diameter of the
capillary tube r (cm) and the distance moved by the manometer fluid h (cm) in a minute
using the formula:

πr2h

Using a respirometer to determine the RQ

Method

Measure oxygen consumption: set up the respirometer and run the experiment with soda-
lime present in both tubes. Use the manometer reading to calculate the change in gas

volume within a given time, x cm3 min-1

Reset the apparatus: allow air to re-enter the tubes via the screw cap and reset the
manometer fluid using the syringe

Run the experiment again: remove the soda-lime from both tubes and use the manometer

reading to calculate the change in gas volume in a given time, y cm3 min-1

Calculations

x tells us the volume of oxygen consumed by respiration within a given time

y tells us the volume of oxygen consumed by respiration within a given time minus the
volume of carbon dioxide produced within a given time
y may be a positive or negative value depending on the direction that the
manometer fluid moves (up = positive value, down = negative value)

The two measurements x and y can be used to calculate the RQ

RQ = CO2 / O2

RQ = (x + y) / x

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12. Energy & Respiration ⬇

Worked example: Calculating RQ from a respirometer experiment

x = 2.9 cm3 min-1

y = -0.8 cm3 min-1

(x + y) / x = RQ

(2.9 – 0.8) / 2.9 = 0.724

When equal volumes of oxygen are consumed and carbon dioxide produced (as seen with glucose)
the manometer fluid will not move and y will be 0, making the RQ 1.

Analysis

Respirometers can be used in experiments to investigate how different factors affect the RQ
of organisms over time
Eg. temperature – using a series of water baths

When an RQ value changes it means the substrate being respired has changed

Some cells may also be using a mixture of substrates in respiration an RQ value of 0.85
suggests both carbohydrates and lipids are being used
This is because the RQ of glucose is 1 and the RQ of lipids is 0.7

Under normal cell conditions the order substrates are used in respiration: carbohydrates,
lipids then proteins

The RQ can also give an indication of under or overfeeding:

An RQ value of more than 1 suggests excessive carbohydrate/calorie intake

An RQ value of less than 0.7 suggests underfeeding

Exam Tip

There are several ways you can manage variables and increase the reliability
of results in respirometer experiments:
• Use a controlled water bath to keep the temperature constant
• Have a control tube with an equal volume of inert material to the volume of
the organisms to compensate for changes in atmospheric pressure
• Repeat the experiment multiple times and use an average

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12. Energy & Respiration ⬇

12.2 RESPIRATION

12.2.1 STRUCTURE & FUNCTION OF MITOCHONDRIA

Structure & Function of the Mitochondria

Mitochondria are rod-shaped organelles 0.5 – 1.0 µm in diameter

They are the site of aerobic respiration in eukaryotic cells

The function of mitochondria is to synthesize ATP

Synthesis of ATP in the mitochondria occurs during the last stage of respiration called
oxidative phosphorylation
This relies on membrane proteins that make up the ‘electron transport chain’ and the
ATP synthase enzyme – the details of this are covered later in the notes

Structure
Mitochondria have two phospholipid membranes

The outer membrane is:

Smooth

Permeable to several small molecules

The inner membrane is:

Folded (cristae)

Less permeable

The site of the electron transport chain (used in oxidative phosphorylation)

Location of ATP synthase (used in oxidative phosphorylation)

The intermembrane space:

Has a low pH due to the high concentration of protons

The concentration gradient across the inner membrane is formed during oxidative
phosphorylation and is essential for ATP synthesis

The matrix:
Is an aqueous solution within the inner membranes of the mitochondrion

Contains ribosomes, enzymes and circular mitochondrial DNA necessary for

mitochondria to function

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12. Energy & Respiration ⬇

Relationship between structure & function

The structure of mitochondria makes them well adapted to their function

They have a large surface area due to the presence of cristae (inner folds) which enables
the membrane to hold many electron transport chain proteins and ATP synthase enzymes

More active cell types can have larger mitochondria with longer and more tightly packed
cristae to enable the synthesis of more ATP because they have a larger surface area

The number of mitochondria in each cell can vary depending on cell activity
Muscle cells are more active and have more mitochondria per cell than fat cells

Exam Tip

Exam questions can sometimes ask you to explain how the structure of a
mitochondrion helps it carry out its function effectively. Make sure to follow
through with your answer. It is not enough to say that cristae increase the
surface area of the inner membrane. You need to explain that an increased
surface area of the inner membrane means there are more electron
transport chain carriers and ATP synthase enzymes which results in
more ATP being produced.
Be prepared to identify the different structures and locations in a
mitochondrion from an electron micrograph.

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12. Energy & Respiration ⬇

12.2.2 THE FOUR STAGES IN AEROBIC RESPIRATION

The Four Stages in Aerobic Respiration

Glucose is the main respiratory substrate used by cells

Aerobic respiration is the process of breaking down a respiratory substrate in order to

produce ATP using oxygen

The process of aerobic respiration using glucose can be split into four stages

Each stage occurs at a particular location in a eukaryotic cell:

Glycolysis takes place in the cell cytoplasm

The Link reaction takes place in the matrix of the mitochondria

The Krebs cycle takes place in the matrix of the mitochondria

Oxidative phosphorylation occurs at the inner membrane of the mitochondria

Four stages of respiration table

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12. Energy & Respiration ⬇

Exam Tip

It’s important to know the exact locations of each stage. It is not enough to
say the Krebs cycle takes place in the mitochondria, you need to say it takes
place in the matrix of the mitochondria.

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12. Energy & Respiration ⬇

12.2.3 AEROBIC RESPIRATION: GLYCOLYSIS

Aerobic Respiration: Glycolysis

Glycolysis is the first stage of respiration

It takes place in the cytoplasm of the cell and involves:

Trapping glucose in the cell by phosphorylating the molecule

Splitting the glucose molecule in two

It results in the production of

2 Pyruvate (3C) molecules

Net gain 2 ATP

2 reduced NAD

Steps of glycolysis
Phosphorylation: glucose (6C) is phosphorylated by 2 ATP to form fructose bisphosphate
(6C)

Glucose + 2ATP → Fructose bisphosphate

Lysis: fructose bisphosphate (6C) splits into two molecules of triose phosphate (3C)

Fructose bisphosphate → 2 Triose phosphate

Oxidation: hydrogen is removed from each molecule of triose phosphate and transferred to
coenzyme NAD to form 2 reduced NAD

4H + 2NAD → 2NADH + 2H+

Dephosphorylation: phosphates are transferred from the intermediate substrate molecules

to form 4 ATP through substrate-linked phosphorylation

4Pi + 4ADP → 4ATP

Pyruvate is produced: the end product of glycolysis which can be used in the next stage of
respiration

2 Triose phosphate → 2 Pyruvate

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12. Energy & Respiration ⬇

Exam Tip

It may seem strange that ATP is used and also produced during glycolysis. At
the start ATP is used to make glucose more reactive (it is usually very
stable) and to lower the activation energy of the reaction. Since 2 ATP are
used and 4 are produced during the process, there is a net gain of 2 ATP
per glucose molecule.

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12. Energy & Respiration ⬇

12.2.4 AEROBIC RESPIRATION: THE LINK REACTION

Entering the Link Reaction

The end product of glycolysis is pyruvate

Pyruvate contains a substantial amount of chemical energy that can be further utilised in
respiration to produce more ATP

When oxygen is available pyruvate will enter the mitochondrial matrix and aerobic
respiration will continue

It moves across the double membrane of the mitochondria via active transport
It requires a transport protein and a small amount of ATP

Once in the mitochondrial matrix pyruvate takes part in the link reaction

The Link Reaction

The link reaction takes place in the matrix of the mitochondria

It is referred to as the link reaction because it links glycolysis to the Krebs cycle

The steps are:

1. Decarboxylation and dehydrogenation of pyruvate by enzymes to produce an acetyl

group, CH3C(O)-

2. Combination with coenzyme A to form acetyl coA

It produces:
Acetyl coA

Carbon dioxide (CO2)

Reduced NAD (NADH)

pyruvate + NAD + CoA → acetyl CoA + carbon dioxide + reduced NAD

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12. Energy & Respiration ⬇

Role of coenzyme A
A coenzyme is a molecule that helps an enzyme carry out its function but is not used in
the reaction itself

Coenzyme A consists of a nucleoside (ribose and adenine) and a vitamin

In the link reaction, CoA binds to the remainder of the pyruvate molecule (acetyl group 2C) to
form acetyl CoA

It then supplies the acetyl group to the Krebs cycle where it is used to continue aerobic
respiration

This is the stage that brings part of the carbohydrate (or lipid/amino acid) into the further
stages of respiration and links the initial stage of respiration in the cytoplasm to the later
stages in the mitochondria

Exam Tip

Remember that there are two pyruvate molecules produced per glucose
molecule so you need to multiply everything by 2 when thinking about
what happens to a single glucose molecule in aerobic respiration.

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12. Energy & Respiration ⬇

12.2.5 AEROBIC RESPIRATION: THE KREBS CYCLE

Outline of the Krebs Cycle

The Krebs cycle (sometimes called the citric acid cycle) consists of a series of enzyme-
controlled reactions

Acetyl CoA (2C) enters the circular pathway via the link reaction

4 carbon (4C) oxaloacetate accepts the 2C acetyl fragment from acetyl CoA to form citrate
(6C)

Citrate is then converted back to oxaloacetate through a series of small reactions

Exam Tip

The Krebs cycle is often referred to as cyclical or circular. This is because the
acceptor molecule oxaloacetate is regenerated throughout the reaction so
that it can start all over again by adding another acetyl CoA.

The Krebs Cycle

Oxaloacetate is regenerated in the Krebs cycle through a series of reactions

Decarboxylation of citrate
Releasing 2 CO2 as waste gas

Dehydrogenation of citrate
Releasing H atoms that reduce coenzymes NAD and FAD

3 NAD and 1 FAD → 3NADH + H+ and 1 FADH2

Substrate-linked phosphorylation
A phosphate is transferred from one of the intermediates to ADP, forming 1 ATP

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12. Energy & Respiration ⬇

Exam Tip

It is a good idea to learn the Krebs cycle in detail. You may be asked to name
the important molecules in the Krebs cycle like oxaloacetate. It is also worth
noting how the number of carbon atoms in the substrate molecule changes
as the cycle progresses.

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12. Energy & Respiration ⬇

12.2.6 AEROBIC RESPIRATION: ROLE OF NAD & FAD

The Role of NAD & FAD

Coenzymes NAD and FAD play a critical role in aerobic respiration

When hydrogen atoms become available at different points during respiration NAD and FAD
accept these hydrogen atoms
A hydrogen atom consists of a hydrogen ion and an electron

When the coenzymes gain a hydrogen they are ‘reduced’

OIL RIG: Oxidation Is Loss, Reduction Is Gain

They transfer the hydrogen atoms (hydrogen ions and electrons) from the different
stages of respiration to the electron transport chain on the inner mitochondrial
membrane, the site where hydrogens are removed from the coenzymes

When the hydrogen atoms are removed the coenzymes are ‘oxidised’

Hydrogen ions and electrons are important in the electron transport chain at the end of
respiration as they play a role in the synthesis of ATP
Electrons from reduced NAD (NADH) and reduced FAD (FADH2) are given to the
electron transport chain

Hydrogen ions from reduced NAD (NADH) and reduced FAD (FADH2) are released
when the electrons are lost

The electron transport chain drives the movement of these hydrogen ions (protons)
across the inner mitochondrial membrane into the mitochondrial matrix, creating a
proton gradient (more hydrogen ions in the matrix)
Movement of hydrogen ions down proton gradient, back into the intermembrane
space, gives the energy required for ATP synthesis

Sources of reduced NAD & FAD

A certain amount of reduced NAD and FAD is produced during the aerobic respiration of a
single glucose molecule

Reduced NAD:
2 x 1 = 2 from Glycolysis

2 x 1 = 2 from the Link Reaction

2 x 3 = 6 from the Krebs cycle

Reduced FAD:
2 x 1 = 2 from the Krebs cycle

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YOUR NOTES
12. Energy & Respiration ⬇

Exam Tip

Note at all stages there is a doubling (2x) of reduced NAD and FAD. This is
because one glucose molecule is split in two in glycolysis and so these
reactions occur twice per single molecule of glucose.

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12. Energy & Respiration ⬇

12.2.7 AEROBIC RESPIRATION: OXIDATIVE PHOSPHORYLATION

Oxidative Phosphorylation

Oxidative phosphorylation is the last stage of aerobic respiration

It takes place at the inner membrane of the mitochondria

Several steps occur:

Hydrogen atoms are donated by reduced NAD and FAD

Hydrogen atoms split into protons and electrons

The high energy electrons release energy as they move through the electron transport
chain
The released energy is used to transport protons across the inner mitochondrial membrane
from the intermembrane space into the matrix

A concentration gradient of protons is established between the intermembrane space and

the matrix

The protons return to the matrix via facilitated diffusion through the channel protein ATP
synthase

The movement of protons down their concentration gradient provides energy for ATP
synthesis

Oxygen combines with protons and electrons at the end of the electron transport chain to
form water

The electron transport chain

The electron transport chain is made up of a series of membrane proteins/ electron
carriers

They are positioned close together which allows the electrons to pass from carrier to carrier

The inner membrane of the mitochondria is impermeable to hydrogen ions so these electron
carriers are required to pump the protons across the membrane to establish the
concentration gradient

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12. Energy & Respiration ⬇

Exam Tip

Examiners often ask why oxygen is so important for aerobic respiration.

Oxygen acts as the final electron acceptor. Without oxygen the electron
transport chain cannot continue as the electrons have nowhere to go. Without
oxygen accepting the electrons (and hydrogens) the reduced coenzymes
NADH and FADH2 cannot be oxidised to regenerate NAD and FAD, so they

can’t be used in further hydrogen transport.

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12. Energy & Respiration ⬇

12.2.8 ANAEROBIC RESPIRATION

Anaerobic Respiration

Sometimes cells experience conditions with little or no oxygen

There are several consequences when there is not enough oxygen available for respiration:
There is no final acceptor of electrons from the electron transport chain

The electron transport chain stops functioning

No more ATP is produced via oxidative phosphorylation

Reduced NAD and FAD aren’t oxidised by an electron carrier

No oxidised NAD and FAD are available for dehydrogenation in the Krebs cycle
The Krebs cycle stops

However, there is still a way for cells to produce some ATP in low oxygen conditions through
anaerobic respiration

Anaerobic pathways
Some cells are able to oxidise the reduced NAD produced during glycolysis so it can be
used for further hydrogen transport

This means that glycolysis can continue and small amounts of ATP are still produced

Different cells use different pathways to achieve this

Yeast and microorganisms use ethanol fermentation

Other microorganisms and mammalian muscle cells use lactate fermentation

Ethanol fermentation
In this pathway reduced NAD transfers its hydrogens to ethanal to form ethanol

In the first step of the pathway pyruvate is decarboxylated to ethanal

Producing CO2

Then ethanal is reduced to ethanol by the enzyme alcohol dehydrogenase

Ethanal is the hydrogen acceptor

Ethanol cannot be further metabolised; it is a waste product

Lactate fermentation
In this pathway reduced NAD transfers its hydrogens to pyruvate to form lactate

Pyruvate is reduced to lactate by enzyme lactate dehydrogenase

Pyruvate is the hydrogen acceptor

The final product lactate can be further metabolised

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12. Energy & Respiration ⬇

Metabolization of lactate
After lactate is produced two things can happen:

1. It can be oxidised back to pyruvate which is then channelled into the Krebs cycle for ATP
production

2. It can be converted into glycogen for storage in the liver

The oxidation of lactate back to pyruvate needs extra oxygen

This extra oxygen is referred to as an oxygen debt

It explains why animals breathe deeper and faster after exercise

Exam Tip

Note that ethanol fermentation is a two-step process (lactate fermentation is

a one-step process). Carbon dioxide is also produced alongside the waste
ethanol. This waste ethanol is what makes yeast vital in making alcoholic
drinks like beer!

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12. Energy & Respiration ⬇

12.2.9 ENERGY YIELD: AEROBIC & ANAEROBIC RESPIRATION

Aerobic & Anaerobic Respiration

In cells there is a much greater energy yield from respiration in aerobic conditions than
in anaerobic conditions

In anaerobic respiration glucose is only partially oxidised meaning only some of its
chemical potential energy is released and transferred to ATP
The only ATP producing reaction that continues is glycolysis (~2 ATP)

As there is no oxygen to act as the final electron acceptor none of the reactions within the
mitochondria can take place
The stages that take place inside the mitochondria produce much more ATP than
glycolysis alone (~36 ATP)

Comparing aerobic & anaerobic respiration table

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12. Energy & Respiration ⬇

Exam Tip

You won’t be expected to know the total yield of ATP from each stage of
respiration in detail but be prepared to explain why aerobic respiration
produces substantially more ATP than anaerobic respiration.

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12. Energy & Respiration ⬇

12.2.10 ANAEROBIC ADAPTATION OF RICE

Anaerobic Adaptations of Rice

Flooding is a major problem when growing crops

As water rises and it covers the different parts of a plant it can create problems:
Plant roots don’t get the oxygen they need for aerobic respiration

Plant leaves don’t get the carbon dioxide they need for photosynthesis

These gases are less readily available in water as they diffuse more slowly in liquid compared
to air

Rice plants possess several adaptations that enable them to survive and grow in waterlogged
conditions

Adaptations for aerobic respiration

Some types of rice show an increased rate of upward growth away from the waterline
The leaves always remain above water so there is access to oxygen and carbon
dioxide through the stomata

Rice plants possess aerenchyma tissue in the stems and roots

This specialised plant tissue contains useful air spaces that allow gases that enter
the stomata to diffuse to other parts of the plant that are above and under the
water

Oxygen and carbon dioxide can therefore be held in this tissue even when underwater
and can be transferred from parts of the plant that has access to air

Adaptations for anaerobic respiration

When there isn’t enough energy being supplied to the cells by aerobic respiration plants
resort to anaerobic respiration as a source of ATP
Plants use ethanol fermentation during anaerobic respiration
Toxic ethanol is produced which can build up in the plant tissue causing damage

Rice plants can tolerate higher levels of toxic ethanol compared to other plants

They also produce more ethanol dehydrogenase

This is the enzyme that breaks down ethanol

The resilience that rice plants have towards ethanol allows them to carry out anaerobic
respiration for longer so enough ATP is produced for the plant to survive and actively grow

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12. Energy & Respiration ⬇

Exam Tip

You might be wondering why farmers would grow rice in paddies (intentionally
flooded fields)?
Growing rice in these conditions actually increases the yield. The plants or
weeds that would usually be competitors for nutrients and light are unable to
survive in these conditions and so the rice has more resources for its growth.

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12. Energy & Respiration ⬇

12.2.11 AEROBIC RESPIRATION: EFFECT OF TEMPERATURE &

SUBSTRATE CONCENTRATION

Effect of Temperature & Substrate Concentration

A redox indicator is a substance that changes colour when it is reduced or oxidised

DCPIP and methylene blue are redox indicators

They are used to investigate the effects of temperature and substrate
concentration on the rate of aerobic respiration in yeast

These dyes can be added to a suspension of living yeast cells as they don’t damage cells

Yeast can respire both aerobically and anaerobically, in this experiment it is their rate of
anaerobic respiration that is being investigated

Mechanism
Dehydrogenation happens regularly throughout the different stages of aerobic respiration

The hydrogens that are removed from substrate molecules are transferred to the final stage
of aerobic respiration, oxidative phosphorylation, via the hydrogen carriers NAD and FAD

When DCPIP and methylene blue are present they can also take up hydrogens and get
reduced

Both redox indicators undergo the same colour change when they are reduced
Blue → colourless

The faster the rate of respiration, the faster the rate of hydrogen release and the faster the
dyes get reduced and change colour
This means that the rate of colour change can correspond to the rate of
respiration in yeast

The rate of respiration is inversely proportional to the time taken

Rate of respiration (sec-1) = 1 / time (sec)

Investigating the effect of temperature & substrate concentration

on the rate of respiration in yeast
The effect of temperature can be investigated by adding the test tubes containing the yeast
suspension to a temperature-controlled water bath and recording the time taken for a
colour change to occur once the dye is added

Repeat across a range of temperatures. For example, 30oC, 35oC, 40oC, 45oC

The effect of substrate concentration can be investigated by adding different

concentrations of a substrate to the suspension of yeast cells and recording the time
taken for a colour change to occur once the dye is added
For example, 0.1% glucose, 0.5% glucose, 1.0% glucose

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12. Energy & Respiration ⬇

Controlling other variables

It is important when investigating one variable to ensure that the other variables in the
experiment are being controlled
Volume of dye added: if there is more dye molecules present then the time taken
for the colour change to occur will be longer

Volume of yeast suspension: when more yeast cells are present the rate of
respiration will be inflated

Type of substrate: yeast cells will respire different substrates at different rates

Concentration of substrate: if there is limited substrate in one tube then the

respiration of those yeast cells will be limited

Temperature: an increase or decrease in temperature can affect the rate of

respiration due to energy demands and kinetic energy changes. The temperature of
the dye being added also needs to be considered

Exam Tip

Although the DCPIP and methylene blue undergo a colour change from blue to
colourless it is important to remember that the yeast suspension in the
test tube may have a slight colour (usually yellow). That means when the
dye changes to colourless there may still be an overall yellow colour in the
test tube. If this is the case it can be useful to have a control tube containing
the same yeast suspension but with no dye added, then you can tell when the
dye has completely changed colour.

Effect of Temperature: Respirometer

Respirometers are used to measure and investigate the rate of oxygen consumption
during aerobic respiration in organisms

By adding the apparatus to a thermostatically controlled water bath the effect of

temperature on the rate of respiration can be investigated

The experiments usually involve organisms such as seeds or invertebrates

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12. Energy & Respiration ⬇

Method
Measure oxygen consumption: set up the respirometer and run the experiment with both
tubes in a controlled temperature water bath. Use the manometer reading to calculate the

change in gas volume within a given time, x cm3 min-1

Reset the apparatus: Allow air to reenter the tubes via the screw cap and reset the
manometer fluid using the syringe. Change the temperature of the water bath and allow
the tubes to acclimate, then close the screw clip to begin the experiment

Run the experiment again: use the manometer reading to calculate the change in gas

volume in a given time, y cm3 min-1

Repeat experiment several times at different temperatures

Calculations
The volume of oxygen consumed (cm3 min-1) can be worked out using the diameter of the
capillary tube r (cm) and the distance moved by the manometer fluid h (cm) in a minute
using the formula:

πr2h

Analysis
The rate of oxygen consumption (cm3 min-1) is often taken as the rate of respiration for
organisms

The different volumes of oxygen consumed obtained for the different temperatures can be
presented in table or graph form to show the effects of temperature

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12. Energy & Respiration ⬇

Exam Tip

If you think back to learning about proteins and enzymes you will remember
that at extreme high temperatures, proteins become denatured and are
unable to carry out their function. At low temperatures, molecules and
enzymes don’t collide very frequently as they don’t have a lot of energy. This
same trend can often be seen in the rate of respiration as the reactions rely
on enzymes.
The respirometer set up above is for measuring the rate of aerobic
respiration. It cannot be used to measure the rate of aerobic respiration as no
oxygen is consumed during aerobic respiration, as shown by the different
equations for aerobic and anaerobic respiration.
Aerobic respiration:
Glucose + Oxygen → Energy + Carbon Dioxide
Anaerobic respiration (in mammals)
Glucose → Energy + Lactic acid

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13. Photosynthesis ⬇

CONTENTS
13.1 Photosynthesis as an Energy Transfer Process
13.1.1 Chloroplasts

13.1.2 Stages of Photosynthesis

13.1.3 Thylakoids & the Stroma

13.1.4 Chloroplast Pigments

13.1.5 Absorption Spectra & Action Spectra

13.1.6 Chromatography of Chloroplast Pigments

13.1.7 Photophosphorylation

13.1.8 The Calvin Cycle

13.2 Investigation of Limiting Factors

13.2.1 Limiting Factors of Photosynthesis

13.2.2 Investigating the Rate of Photosynthesis

13.1 PHOTOSYNTHESIS AS AN ENERGY TRANSFER

PROCESS

13.1.1 CHLOROPLASTS

Chloroplast Structures & their Functions

Chloroplasts are the organelles in plant cells where photosynthesis occurs

Each chloroplast is surrounded by a double-membrane envelope

Each of the envelope membranes is a phospholipid bilayer

Chloroplasts are filled with a fluid known as the stroma

The stroma is the site of the light-independent stage of photosynthesis

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13. Photosynthesis ⬇

A separate system of membranes is found in the stroma

This membrane system is the site of the light-dependent stage of photosynthesis

The membrane contains the pigments, enzymes and electron carriers required for
the light-dependent reactions

This membrane system consists of a series of flattened fluid-filled sacs known as

thylakoids

These thylakoids stack up to form structures known as grana (singular – granum)

Grana are connected by membranous channels called stroma lamellae, which ensure
the stacks of sacs are connected but distanced from each other

The membranes of the grana create a large surface area to increase the number
of light-dependent reactions that can occur

This membrane system provides a large number of pigment molecules in an

arrangement that ensures as much light as necessary is absorbed

The stroma also contains small (70S) ribosomes, a loop of DNA and starch grains:
The loop of DNA codes for some of the chloroplast proteins (other chloroplast
proteins are coded for by the DNA in the plant cell nucleus)

The proteins coded for by this loop of chloroplast DNA are produced at the 70S
ribosomes

Sugars formed during photosynthesis are stored as starch inside starch grains

Exam Tip

Make sure you can identify the structures of a chloroplast on a diagram AND
that you can explain the function of each of these structures.

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13. Photosynthesis ⬇

13.1.2 STAGES OF PHOTOSYNTHESIS

The Two Stages of Photosynthesis

Photosynthesis occurs in two stages: the light-dependent stage, which takes place in the
thylakoids, and the light-independent stage, which takes place in the stroma

During the light-dependent stage of photosynthesis:

Reduced NADP is produced when hydrogen ions combine with the carrier
molecule NADP using electrons from the photolysis of water

ATP is produced (from ADP and Pi by ATP synthase in a process called

photophosphorylation (ADP + Pi → ATP)

Photophosphorylation uses the proton (H+) gradient generated by the photolysis of

water

Energy from ATP and hydrogen from reduced NADP are passed from the light-
dependent stage to the light-independent stage of photosynthesis

The energy and hydrogen are used during the light-independent reactions (known
collectively as the Calvin cycle) to produce complex organic molecules, including (but not
limited to) carbohydrates, such as:
Starch (for storage)

Sucrose (for translocation around the plant)

Cellulose (for making cell walls)

Exam Tip

Remember, the whole purpose of the light-dependent reactions is to produce

ATP and reduced NADP, which are then used to complete the process of
photosynthesis through the light-independent reactions.

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13. Photosynthesis ⬇

13.1.3 THYLAKOIDS & THE STROMA

Thylakoids & the Stroma

Plant cells contain chloroplasts which is the site of photosynthesis

Chloroplasts are filled with a fluid known as the stroma

The system of membranes found in the stroma of the chloroplast consists of a series of
flattened fluid-filled sacs known as thylakoids

In places, these thylakoids stack up to form structures known as grana (singular – granum)

The light-dependent stage of photosynthesis occurs in the thylakoid membranes and

the thylakoid spaces (the spaces inside the thylakoids)

The thylakoid membranes contain the pigments, enzymes and electron carriers required
for the light-dependent reactions

The membranes of the grana create a large surface area to increase the number of
light-dependent reactions that can occur

This membrane system provides a large number of pigment molecules in an arrangement

that ensures as much light as necessary is absorbed

The pigment molecules are arranged in light-harvesting clusters known as photosystems

In a photosystem, the different pigment molecules are arranged in funnel-like structures

the thylakoid membrane (each pigment molecule passes energy down to the next pigment
molecule in the cluster until it reaches the primary pigment reaction centre)

The stroma is the fluid that fills the chloroplasts and surrounds thylakoids

CO2, sugars, enzymes and other molecules are dissolved in the stroma

The stroma is the site of the light-independent stage of photosynthesis

Exam Tip

Don’t get confused between the light-dependent and light-independent

reactions – you need to know where each of these sets of reactions occurs.
The photosynthetic pigments required to absorb light energy are only found in
the thylakoid membranes, meaning that the reactions that occur here are
dependent on light (light-dependent)!

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13. Photosynthesis ⬇

13.1.4 CHLOROPLAST PIGMENTS

Chloroplast Pigments

Chloroplasts contain several different photosynthetic pigments within the thylakoids,

which absorb different wavelengths of light
In places, these thylakoids stack up to form structures known as grana (singular –
granum)

The thylakoid membrane system provides a large number of pigment molecules in an

arrangement that ensures as much light as necessary is absorbed

The pigment molecules are arranged in light-harvesting clusters known as

photosystems
In a photosystem, the different pigment molecules are arranged in funnel-like
structures the thylakoid membrane (each pigment molecule passes energy down to
the next pigment molecule in the cluster until it reaches the primary pigment reaction
centre)

The light-dependent stage of photosynthesis occurs in the thylakoid membranes and

the thylakoid spaces (the spaces inside the thylakoids)

This is why the thylakoid membranes contain the pigments, enzymes and electron
carriers required for the light-dependent reactions

There are two groups of pigments: primary pigments known as chlorophylls and accessory
pigments known as carotenoids

Chloroplast pigments table

Chlorophylls absorb wavelengths in the blue-violet and red regions of the light spectrum
They reflect green light, causing plants to appear green

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13. Photosynthesis ⬇

Carotenoids absorb wavelengths of light mainly in the blue-violet region of the spectrum

Exam Tip

Remember – the pigments themselves have colour (as described in the table).
This is different from the colours of light that they absorb.

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13. Photosynthesis ⬇

13.1.5 ABSORPTION SPECTRA & ACTION SPECTRA

Absorption Spectra & Action Spectra

An absorption spectrum is a graph that shows the absorbance of different wavelengths of

light by a particular pigment

Chlorophylls absorb wavelengths in the blue-violet and red regions of the light spectrum

Carotenoids absorb wavelengths of light mainly in the blue-violet region of the spectrum

An action spectrum is a graph that shows the rate of photosynthesis at different

wavelengths of light

The rate of photosynthesis is highest at the blue-violet and red regions of the light
spectrum, as these are the wavelengths of light that plants can absorb (ie. the wavelengths
of light that chlorophylls and carotenoids can absorb)

There is a strong correlation between the cumulative absorption spectra of all pigments and
the action spectrum:
Both graphs have two main peaks – at the blue-violet region and the red region of
the light spectrum

Both graphs have a trough in the green-yellow region of the light spectrum

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13. Photosynthesis ⬇

13.1.6 CHROMATOGRAPHY OF CHLOROPLAST PIGMENTS

Chromatography of Chloroplast Pigments

Chromatography is an experimental technique that is used to separate mixtures:

The mixture is dissolved in a fluid/solvent (called the mobile phase) and the
dissolved mixture then passes through a static material (called the stationary phase)

Different components within the mixture travel through the material at different
speeds

This causes the different components to separate

A retardation factor (Rf) can be calculated for each component of the mixture

Rf value = distance travelled by component ÷ distance travelled by solvent

Two of the most common techniques for separating these photosynthetic pigments are:
Paper chromatography – the mixture of pigments is passed through paper
(cellulose)

Thin-layer chromatography – the mixture of pigments is passed through a thin

layer of adsorbent (eg. silica gel), through which the mixture travels faster and
separates more distinctly

Chromatography can be used to separate and identify chloroplast pigments that have been
extracted from a leaf as each pigment will have a unique Rf value

The Rf value demonstrates how far a dissolved pigment travels through the stationary phase
A smaller Rf value indicates the pigment is less soluble and larger in size

Although specific Rf values depend on the solvent that is being used, in general:
Carotenoids have the highest Rf values (usually close to 1)

Chlorophyll b has a much lower Rf value

Chlorophyll a has an Rf value somewhere between those of carotenoids and

chlorophyll b

The Rf value demonstrates how far a

Small Rf values indicate the pigment is less soluble and larger in size

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13. Photosynthesis ⬇

Exam Tip

Make sure you learn the approximate Rf values for the different pigments

within chloroplasts (or at least their values relative to each other). This means
you should be able to identify different chloroplast pigments based on their Rf

values alone.

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13. Photosynthesis ⬇

13.1.7 PHOTOPHOSPHORYLATION

Types of Photophosphorylation

The thylakoid membrane is the site of the light-dependent stage of photosynthesis

During the light-dependent stage of photosynthesis:

Light energy is used to breakdown water (photolysis) to produce hydrogen ions,
electrons and oxygen in the thylakoid lumen

A proton gradient is formed due to the photolysis of water resulting in a high

concentration of hydrogen ions in the thylakoid lumen

Electrons travel through an electron transport chain of proteins within the

membrane
Reduced NADP (NADPH) is produced when hydrogen ions in the stroma and
electrons from the electron transport chain combine with the carrier molecule
NADP

ATP is produced during a process known as photophosphorylation (ADP + Pi → ATP)

using the proton gradient between the thylakoid lumen and stroma to drive the
enzyme ATP synthase

The photophosphorylation of ADP to ATP can be cyclic or non-cyclic, depending on the

pattern of electron flow in photosystem I or photosystem II or both
In cyclic photophosphorylation, only photosystem I is involved

In non-cyclic photophosphorylation, both photosystem I and photosystem II are

involved

Photosystems are collections of photosynthetic pigments that absorb light energy and
transfer the energy onto electrons, each photosystem contains a primary pigment
Photosystem II has a primary pigment that absorbs light at a wavelength of 680nm
and is therefore called P680

Photosystem II is at the beginning of the electron transport chain and is where the
photolysis of water takes place

Photosystem II has a primary pigment that absorbs light at a wavelength of 700nm

and is therefore called P700

Photosystem I is in the middle of the electron transport chain

The energy carried by the ATP is then used during the light-independent reactions of
photosynthesis

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YOUR NOTES
13. Photosynthesis ⬇

Cyclic Photophosphorylation

Cyclic photophosphorylation involves photosystem I (PSI) only

Light is absorbed by photosystem I (located in the thylakoid membrane) and passed to the
photosystem I primary pigment (P700)

An electron in the primary pigment molecule (ie. the chlorophyll molecule) is excited to a
higher energy level and is emitted from the chlorophyll molecule in a process known as
photoactivation

This excited electron is captured by an electron acceptor, transported via a chain of

electron carriers known as an electron transport chain before being passed back to the
chlorophyll molecule in photosystem I (hence: cyclic)

As electrons pass through the electron transport chain they provide energy to transport

protons (H+) from the stroma to the thylakoid lumen via a proton pump

A build-up of protons in the thylakoid lumen can then be used to drive the synthesis of ATP
from ADP and an inorganic phosphate group (Pi) by the process of chemiosmosis

Chemiosmosis is the movement of chemicals (protons) down their concentration gradient,

the energy released from this can be used by ATP synthase to synthesise ATP

The ATP then passes to the light-independent reactions

Exam Tip

Make sure you know the difference between the two forms of
photophosphorylation!
Cyclic photophosphorylation differs from non-cyclic photophosphorylation in
two key ways:
• Cyclic photophosphorylation only involves photosystem I (whereas non-
cyclic photophosphorylation involves photosystems I and II)
• Cyclic photophosphorylation does not produce reduced NADP (whereas non-
cyclic photophosphorylation does)

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YOUR NOTES
13. Photosynthesis ⬇

Non-Cyclic Photophosphorylation

Non-cyclic photophosphorylation involves both photosystem I (PSI) and photosystem II

(PSII)

Photosystem II
Light is absorbed by photosystem II (located in the thylakoid membrane) and passed to
the photosystem II primary pigment (P680)

An electron in the primary pigment molecule (ie. the chlorophyll molecule) is excited to a
higher energy level and is emitted from the chlorophyll molecule in a process known as
photoactivation

This excited electron is passed down a chain of electron carriers known as an electron
transport chain, before being passed on to photosystem I

During this process to ATP is synthesised from ADP and an inorganic phosphate group (Pi)
by the process of chemiosmosis

The ATP then passes to the light-independent reactions

Photosystem II contains a water-splitting enzyme called the oxygen-evolving complex

which catalyses the breakdown (photolysis) of water by light:

H2O → 2H+ + 2e– + ½O2

As the excited electrons leave the primary pigment of photosystem II and are passed on to
photosystem I, they are replaced by electrons from the photolysis of water

Photosystem I
At the same time as photoactivation of electrons in photosystem II, electrons in
photosystem I also undergo photoactivation

The excited electrons from photosystem I also pass along an electron transport chain

These electrons combine with hydrogen ions (produced by the photolysis of water) and the
carrier molecule NADP to give reduced NADP:

2H+ + 2e– + NADP → reduced NADP

The reduced NADP (NADPH) then passes to the light-independent reactions to be used in
the synthesis of carbohydrate

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YOUR NOTES
13. Photosynthesis ⬇

Exam Tip

Remember – the oxygen produced during the photolysis of water is a waste

product of this process. The hydrogen ions and electrons produced during the
photolysis of water are useful products.
The electrons replace those that have been lost from the primary pigment
molecule of photosystem II (as photosystem II passes its electrons on to
photosystem I). The hydrogen ions combine with the electrons from
photosystem I to form reduced NADP (NADPH).

Photophosphorylation & Chemiosmosis

During photophosphorylation, energetic (excited) electrons are captured by an electron

acceptor in a thylakoid membrane

These excited electrons are then passed along a chain of electron carriers (known as the
electron transport chain)

The electron carriers are alternately reduced (as they gain an electron) and then oxidised
(as they lose the electron by passing it to the next carrier)

The excited electrons gradually release their energy as they pass through the electron
transport chain

The released energy is used to actively transport protons (H+ ions) across the thylakoid
membrane, from the stroma (the fluid within chloroplasts) to the thylakoid lumen (the
space within thylakoids)

A ‘proton pump’ transports the protons across the thylakoid membrane, from the stroma to
the thylakoid lumen

This creates a proton gradient, with a high concentration of protons in the thylakoid
lumen and a low concentration in the stroma

Protons then return to the stroma (moving down the proton concentration gradient) by
facilitated diffusion through transmembrane ATP synthase enzymes in a process
known as chemiosmosis

This process provides the energy needed to synthesise ATP by adding an inorganic
phosphate group (Pi) to ADP (ADP + Pi → ATP)

The whole process is known as photophosphorylation as light provides the initial energy
source for ATP synthesis

After being passed down the electron transport chain, the de-energised electrons from
photosystem II are taken up by photosystem I

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YOUR NOTES
13. Photosynthesis ⬇

Exam Tip

Make sure you understand the direction of movement of protons across the
thylakoid membrane during photophosphorylation. Protons are first actively
transferred from the stroma to the thylakoid space. These protons then move
from the thylakoid space back to the stroma during chemiosmosis.

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YOUR NOTES
13. Photosynthesis ⬇

13.1.8 THE CALVIN CYCLE

Stages of the Calvin Cycle

Energy from ATP and hydrogen from reduced NADP are passed from the light-
dependent stage to the light-independent stage of photosynthesis

The energy and hydrogen are used during the light-independent reactions (known
collectively as the Calvin cycle) to produce complex organic molecules, including (but not
limited to) carbohydrates, such as:
Starch (for storage)

Sucrose (for translocation around the plant)

Cellulose (for making cell walls)

This stage of photosynthesis does not, in itself, require energy from light (hence light-
independent) and can therefore take place in light or darkness. However, as it requires
inputs of ATP and reduced NADP from the light-dependent stage, the Calvin cycle cannot
continue indefinitely in darkness, as these inputs will run out

There are three main steps within the Calvin cycle:

Rubisco catalyses the fixation of carbon dioxide by combination with a molecule
of ribulose bisphosphate (RuBP), a 5C compound, to yield two molecules of
glycerate 3-phosphate (GP), a 3C compound

GP is reduced to triose phosphate (TP) in a reaction involving reduced NADP and

ATP

RuBP is regenerated from TP in reactions that use ATP

Carbon fixation
Carbon dioxide combines with a five-carbon (5C) sugar known as ribulose bisphosphate
(RuBP)

An enzyme called rubisco (ribulose bisphosphate carboxylase) catalyses this reaction

The resulting six-carbon (6C) compound is unstable and splits in two

This gives two molecules of a three-carbon (3C) compound known as glycerate 3-

phosphate (GP)

The carbon dioxide has been ‘fixed’ (it has been removed from the external environment
and has become part of the plant cell)

Glycerate 3-phosphate (GP) is not a carbohydrate but the next step in the Calvin cycle
convert it into one

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YOUR NOTES
13. Photosynthesis ⬇

Reduction of glycerate 3-phosphate

Energy from ATP and hydrogen from reduced NADP – both produced during the light-
dependent stage of photosynthesis – are used to reduce glycerate 3-phosphate (GP) to a
phosphorylated three-carbon (3C) sugar known as triose phosphate (TP)

One-sixth of the triose phosphate (TP) molecules are used to produce useful organic
molecules needed by the plant:
Triose phosphates can condense to become hexose phosphates (6C), which can be
used to produce starch, sucrose or cellulose

Triose phosphates can be converted to glycerol and glycerate 3-phosphates to fatty

acids, which join to form lipids for cell membranes

Triose phosphates can be used in the production of amino acids for protein
synthesis

Regeneration of ribulose bisphosphate

Five-sixths of the triose phosphate (TP) molecules are used to regenerate ribulose
bisphosphate (RuBP)

This process requires ATP

Calvin Cycle Intermediates

Intermediate molecules of the Calvin cycle (such as glycerate 3-phosphate and triose
phosphate) are used to produce other molecules

Glycerate 3-phosphate (GP) is used to produce some amino acids

Triose phosphate (TP) is used to produce:

Hexose phosphates (6C), which can be used to produce starch, sucrose or
cellulose

Lipids for cell membranes

Amino acids for protein synthesis

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13. Photosynthesis ⬇

13.2 INVESTIGATION OF LIMITING FACTORS

13.2.1 LIMITING FACTORS OF PHOTOSYNTHESIS

Limiting Factors of Photosynthesis

Plants need several factors for photosynthesis to occur:

the presence of photosynthetic pigments

a supply of carbon dioxide

a supply of water

light energy

a suitable temperature

If there is a shortage of any of these factors, photosynthesis cannot occur at its maximum
possible rate

The main external factors that affect the rate of photosynthesis are:
light intensity

carbon dioxide concentration

temperature

These are known as limiting factors of photosynthesis

If any one of these factors is below the optimum level for the plant, its rate of
photosynthesis will be reduced, even if the other two factors are at the optimum level

Exam Tip

Light intensity, CO2 concentration and temperature are the three limiting

factors of photosynthesis that you need to learn. Although a lack of water can
reduce the rate of photosynthesis, water shortages usually affect other
processes in the plant before affecting photosynthesis.

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YOUR NOTES
13. Photosynthesis ⬇

Limiting Factors of Photosynthesis: Effects

Changes in light intensity, carbon dioxide concentration and temperature are all
limiting factors that affect the rate of photosynthesis:

Light intensity
When temperature and carbon dioxide concentration remain constant, changes in light
intensity affect the rate of photosynthesis

The rate of photosynthesis increases as light intensity increases:

The greater the light intensity, the more energy supplied to the plant and therefore
the faster the light-dependent stage of photosynthesis can occur

This produces more ATP and reduced NADP for the Calvin cycle (light-
independent stage), which can then also occur at a greater rate

During this stage of the graph below, light intensity is said to be a limiting factor of
photosynthesis

At some point, if light intensity continues to increase, the relationship above will no longer
apply and the rate of photosynthesis will reach a plateau

At this point, light intensity is no longer a limiting factor of photosynthesis – another

factor is limiting the rate of photosynthesis

The factors which could be limiting the rate when the line on the graph is horizontal include
temperature being too low or too high, or not enough carbon dioxide

Carbon dioxide concentration

The rate of photosynthesis increases as carbon dioxide concentration increases:
Carbon dioxide is one of the raw materials required for photosynthesis

It is required for the light-independent stage of photosynthesis, when CO2 is

combined with the five-carbon compound ribulose bisphosphate (RuBP)

This means the more carbon dioxide that is present, the faster this step of the Calvin
cycle can occur and the faster the overall rate of photosynthesis

This trend will continue until some other factor required for photosynthesis prevents the rate
from increasing further because it is in short supply

The factors which could be limiting the rate when the line on the graph is horizontal include
temperature being too low or too high, or not enough light

Temperature
As temperature increases the rate of photosynthesis increases as the reaction is
controlled by enzymes

However, as the reaction is controlled by enzymes, this trend only continues up to a

certain temperature beyond which the enzymes begin to denature and the rate of
reaction decreases

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13. Photosynthesis ⬇

For most metabolic reactions, temperature has a large effect on reaction rate

For photosynthesis, temperature has no significant effect on the light-dependent

reactions, as these are driven by energy from light rather than the kinetic energy of the
reacting molecules

However, the Calvin cycle is affected by temperature, as the light-independent

reactions are enzyme-controlled reactions (eg. rubisco catalyses the reaction between
CO2 and the five-carbon compound ribulose bisphosphate)

Exam Tip

Interpreting graphs of limiting factors can be confusing for many students, but
it’s quite simple.
In the section of the graph where the rate is increasing (the line is going up),
the limiting factor is whatever the label on the x-axis (the bottom axis) of the
graph is.
In the section of the graph where the rate is not increasing (the line is
horizontal), the limiting factor will be something other than what is on the x-
axis – choose from temperature, light intensity or carbon dioxide
concentration.

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YOUR NOTES
13. Photosynthesis ⬇

13.2.2 INVESTIGATING THE RATE OF PHOTOSYNTHESIS

Investigating the Rate of Photosynthesis: Redox Indicators

The light-dependent reactions of photosynthesis take place in the thylakoid membrane

and involve the release of high-energy electrons from chlorophyll a molecules

These electrons are picked up by electron acceptors and then passed down the electron
transport chain

However, if a redox indicator (such as DCPIP or methylene blue) is present, the indicator
takes up the electrons instead

This causes the indicator to change colour

DCPIP: oxidised (blue) → accepts electrons → reduced (colourless)
Methylene blue: oxidised (blue) → accepts electrons → reduced (colourless)

The colour of the reduced solution may appear green because the chlorophyll have a
green colour

The rate at which the redox indicator changes colour from its oxidised state to its reduced
state can be used as a measure of the rate of photosynthesis
When light is at a higher intensity, or at more preferable light wavelengths, the rate of
photoactivation of electrons is faster, therefore the rate of reduction of the indicator is
faster

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13. Photosynthesis ⬇

Method
Step 1:
Leaves are crushed in a liquid known as an isolation medium

This produces a concentrated leaf extract that contains a suspension of intact and
functional chloroplasts

The medium must have the same water potential as the leaf cells (so the chloroplasts
don’t shrivel or burst) and contain a buffer (to keep the pH constant). It should also be ice-
cold (to avoid damaging the chloroplasts and to maintain membrane structure)

Step 2:
Small tubes are set up with different intensities, or different colours (wavelengths) of
light shining of them

If different intensities of light are used, they must all be of the same wavelength (same
colour of light)

If different wavelengths of light are used, they must all be of the same light intensity

Step 3:
DCPIP of methylene blue indicator is added to each tube, as well as a small volume of the
leaf extract

Step 4:
The time taken for the redox indicator to go colourless is recorded

This is a measure of the rate of photosynthesis

Exam Tip

In chemistry the acronym ‘OILRIG’ is used to remember if something is being

oxidised or reduced. Oxidation Is Loss (of electrons) and Reduction Is Gain (of
electrons). Therefore the oxidised state is when it hasn’t accepted electrons
and the reduced state has accepted electrons.

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YOUR NOTES
13. Photosynthesis ⬇

Investigating the Rate of Photosynthesis: Aquatic Plants

Investigations to determine the effects of light intensity, carbon dioxide concentration and
temperature on the rate of photosynthesis can be carried out using aquatic plants, such
as Elodea or Cabomba (types of pondweed)

The effect of these limiting factors on the rate of photosynthesis can be investigated in the
following ways:
Light intensity – change the distance (d) of a light source from the plant (light

intensity is proportional to 1/d2)

Carbon dioxide concentration – add different quantities of sodium

hydrogencarbonate (NaHCO3) to the water surrounding the plant, this dissolves to
produce CO2

Temperature (of the solution surrounding the plant) – place the boiling tube
containing the submerged plant in water baths of different temperatures

Whilst changing one of these factors during the investigation (as described below), ensure
the other two remain constant
For example, when investigating the effect of light intensity on the rate of
photosynthesis, a glass tank should be placed in between the lamp and the boiling
tube containing the pondweed to absorb heat from the lamp – this prevents the
solution surrounding the plant from changing temperature

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13. Photosynthesis ⬇

Method
Step 1:
Ensure the water is well aerated before use by bubbling air through it

This will ensure oxygen gas given off by the plant during the investigation form bubbles and
do not dissolve in the water

Step 2:
Ensure the plant has been well illuminated before use

This will ensure that the plant contains all the enzymes required for photosynthesis and that
any changes of rate are due to the independent variable

Step 3:
Set up the apparatus in a darkened room

Ensure the pondweed is submerged in sodium hydrogencarbonate solution (1%) – this

ensures the pondweed has a controlled supply of carbon dioxide (a reactant in
photosynthesis)

Step 4:
Cut the stem of the pondweed cleanly just before placing into the boiling tube

Step 5:
Measure the volume of gas collected in the gas-syringe in a set period of time (eg. 5
minutes)

Step 6:
Change the independent variable (ie. change the light intensity, carbon dioxide
concentration or temperature depending on which limiting factor you are investigating) and
repeat step 5

Step 7:
Record the results in a table and plot a graph of volume of oxygen produced per minute
against the distance from the lamp (if investigating light intensity), carbon dioxide
concentration, or temperature

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YOUR NOTES
13. Photosynthesis ⬇

Exam Tip

Learn the 3 limiting factors and how each one can be altered in an laboratory
environment:
Light intensity – the distance of the light source from the plant (intensity ∝

1/d2)
Temperature – changing the temperature of the water bath the test tube sits
in
Carbon dioxide – the amount of NaHCO3 dissolved in the water the pondweed

is in
Also remember that the variables not being tested (the control variables)
must be kept constant.

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14. Homeostasis ⬇

CONTENTS
14.1 Homeostasis in Mammals
14.1.1 Homeostasis

14.1.2 Production of Urea

14.1.3 Kidney Structure

14.1.4 Nephron Structure

14.1.5 Formation of Urine

14.1.6 Osmoregulation

14.1.7 The Control of Blood Glucose

14.1.8 Test Strips & Biosensors

14.2 Homeostasis in Plants

14.2.1 Stomata

14.2.2 Guard Cells

14.2.3 Abscisic Acid & Stomatal Closure

14.1 HOMEOSTASIS IN MAMMALS

14.1.1 HOMEOSTASIS

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14. Homeostasis ⬇

Homeostasis

In order to function properly and efficiently, organisms have different control systems
that ensure their internal conditions are kept relatively constant

The process of maintaining constant internal body conditions is known as homeostasis

Homeostasis is critically important for organisms as it ensures the maintenance of

optimal conditions for enzyme action and cell function

Sensory cells can detect information about the conditions inside and outside of the body

Examples of physiological factors that are controlled by homeostasis in mammals

include:
Core body temperature

Metabolic waste (eg. carbon dioxide and urea)

Blood pH

Concentration of glucose in the blood

Water potential of the blood

Concentration of the respiratory gases (carbon dioxide and oxygen) in the blood

Exam Tip

Learn the following definition for homeostasis:

Homeostasis is the regulation of the internal conditions of a cell or organism
to maintain optimum conditions for function, in response to internal and
external changes.

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14. Homeostasis ⬇

Principles of Homeostasis

The majority of homeostatic control mechanisms in organisms use negative feedback to

maintain homeostatic balance (ie. to keep certain physiological factors, such as blood
glucose concentration, within certain limits)

Negative feedback control loops involve:

A receptor (or sensor) – to detect a stimulus that is involved with a condition /
physiological factor

A coordination system (nervous system and endocrine system) – to transfer

information between different parts of the body

An effector (muscles and glands) – to carry out a response

Outcome of a negative feedback loop:

The factor / stimulus is continuously monitored

If there is an increase in the factor, the body responds to make the factor decrease

If there is a decrease in the factor, the body responds to make the factor increase

Homeostasis in mammals relies on two different coordination systems to transfer

information between different parts of the body:
Nervous system – information is transmitted as electrical impulses that travel
along neurones

Endocrine system – information is transmitted as chemical messengers called

hormones that travel in the blood

Exam Tip

Although the nervous and endocrine systems are both important in

homeostasis and the regulation of certain physiological factors, there are
some fundamental differences between them.
Information is transmitted through these two systems in different ways
(electrical impulses vs. hormones). Also, the nervous system is usually
required for fast, but short-lived responses, whereas the endocrine system is
involved in slower, but longer-lasting responses (although this is not always
the case and some hormones can act very quickly)!

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14. Homeostasis ⬇

14.1.2 PRODUCTION OF UREA

Production of Urea

Many metabolic reactions within the body produce waste products

The removal of these waste products is known as excretion

Many excretory products are formed in humans, with two in particular (carbon dioxide and
urea) being formed in much greater quantities than others

Urea
Urea is produced in the liver

It is produced from excess amino acids

If more protein is eaten than is required, the excess cannot be stored in the body

However, the amino acids within the protein can still provide useful energy

To make this energy accessible, the amino group is removed from each amino acid

This process is known as deamination:

The amino group (-NH2) of an amino acid is removed, together with an extra
hydrogen atom

These combine to form ammonia (NH3)

The remaining keto acid may enter the Krebs cycle to be respired, be converted to
glucose, or converted to glycogen / fat for storage

Ammonia is a very soluble and highly toxic compound that is produced during
deamination. It can be very damaging if allowed to build up in the blood

This is avoided by converting ammonia to urea

Urea is less soluble and less toxic than ammonia

Ammonia is combined with carbon dioxide to form urea

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14. Homeostasis ⬇

14.1.3 KIDNEY STRUCTURE

Structure of the Human Kidney

Humans have two kidneys

The kidneys are responsible for carrying out two very important functions:
As an osmoregulatory organ – they regulate the water content of the blood
(vital for maintaining blood pressure)

As an excretory organ – they excrete the toxic waste products of metabolism

(such as urea) and substances in excess of requirements (such as salts)

The position of the kidneys and their associated structures

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14. Homeostasis ⬇

The function of the kidneys & their associated structures table

The kidney itself is surrounded by a fairly tough outer layer known as the fibrous capsule

Beneath the fibrous capsule, the kidney has three main areas:
The cortex (contains the glomerulus, as well as the Bowman’s capsule, proximal
convoluted tubule, and distal convoluted tubule of the nephrons)

The medulla (contains the loop of Henle and collecting duct of the nephrons)

The renal pelvis (where the ureter joins the kidney)

Exam Tip

Make sure you can identify all the structures mentioned on this page if you
are presented with a diagram of the kidney and its associated structures, or a
diagram with a vertical cross-section of the kidney itself.

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14. Homeostasis ⬇

14.1.4 NEPHRON STRUCTURE

Nephron Structure

Each kidney contains thousands of tiny tubes, known as nephrons

The nephron is the functional unit of the kidney – the nephrons are responsible for the
formation of urine

There is also a network of blood vessels associated with each nephron:

Within the Bowman’s capsule of each nephron is a structure known as the
glomerulus

Each glomerulus is supplied with blood by an afferent arteriole (which carries blood
from the renal artery)

The capillaries of the glomerulus rejoin to form an efferent arteriole

Blood then flows from the efferent arteriole into a network of capillaries that run
closely alongside the rest of the nephron

Blood from these capillaries eventually flows into the renal vein

Exam Tip

As well as in diagrams, you should be able to identify the parts of the nephron
described above in photomicrographs and electron micrographs too
(examples of these can be found in your Cambridge International AS & A
Level coursebook).

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14. Homeostasis ⬇

14.1.5 FORMATION OF URINE

Formation of Urine in the Nephron

The nephron is the functional unit of the kidney – the nephrons are responsible for the
formation of urine

The process of urine formation in the kidneys occurs in two stages:

1. Ultrafiltration

2. Selective reabsorption

The two stages of urine production in the kidneys table

After the necessary reabsorption of amino acids, water, glucose and inorganic ions is
complete (even some urea is reabsorbed), the filtrate eventually leaves the nephron
and is now referred to as urine

This urine then flows out of the kidneys, along the ureters and into the bladder, where it is
temporarily stored

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14. Homeostasis ⬇

Ultrafiltration

The blood in the glomerular capillaries is separated from the lumen of the Bowman’s
capsule by two cell layers with a basement membrane in between them:
The first cell layer is the endothelium of the capillary – each capillary endothelial
cell is perforated by thousands of tiny membrane-lined circular holes

The next layer is the basement membrane – this is made up of a network of

collagen and glycoproteins

The second cell layer is the epithelium of the Bowman’s capsule – these epithelial
cells have many tiny finger-like projections with gaps in between them and are known
as podocytes

As blood passes through the glomerular capillaries, the holes in the capillary endothelial cells
and the gaps between the podocytes allows substances dissolved in the blood plasma to
pass into the Bowman’s capsule
The fluid that filters through from the blood into the Bowman’s capsule is known as
the glomerular filtrate

The main substances that pass out of the capillaries and form the glomerular filtrate

are: amino acids, water, glucose, urea and inorganic ions (mainly Na+, K+ and

Cl–)

Red and white blood cells and platelets remain in the blood as they are too large to
pass through the holes in the capillary endothelial cells

The basement membrane acts as a filter as it stops large protein molecules from
getting through

How ultrafiltration occurs

Ultrafiltration occurs due to the differences in water potential between the plasma in the
glomerular capillaries and the filtrate in the Bowman’s capsule
Remember – water moves down a water potential gradient, from a region of higher
water potential to a region of lower water potential. Water potential is increased by
high pressure and decreased by the presence of solutes

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14. Homeostasis ⬇

Ultrafiltration & selective reabsorption table

Overall, the effect of the pressure gradient outweighs the effect of solute gradient

Therefore, the water potential of the blood plasma in the glomerulus is higher than the
water potential of the filtrate in the Bowman’s capsule

This means that as blood flows through the glomerulus, there is an overall movement of
water down the water potential gradient from the blood into the Bowman’s
capsule

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14. Homeostasis ⬇

Selective Reabsorption

Many of the substances that end up in the glomerular filtrate actually need to be kept by
the body

These substances are reabsorbed into the blood as the filtrate passes along the nephron

This process is knowns as selective reabsorption as only certain substances are

reabsorbed

Most of this reabsorption occurs in the proximal convoluted tubule

The lining of the proximal convoluted tubule is composed of a single layer of epithelial cells,
which are adapted to carry out reabsorption in several ways:
Microvilli

Co-transporter proteins

A high number of mitochondria

Tightly packed cells

Adaptations for selective reabsorption table

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14. Homeostasis ⬇

How selective reabsorption occurs

Blood capillaries are located very close to the outer surface of the proximal convoluted tubule
As the blood in these capillaries comes straight from the glomerulus, it has very little
plasma and has lost much of its water, inorganic ions and other small solutes

The basal membranes (of the proximal convoluted tubule epithelial cells) are the sections of
the cell membrane that are closest to the blood capillaries

Sodium-potassium pumps in these basal membranes move sodium ions out of the
epithelial cells and into the blood, where they are carried away

This lowers the concentration of sodium ions inside the epithelial cells, causing
sodium ions in the filtrate to diffuse down their concentration gradient through the luminal
membranes (of the epithelial cells)

These sodium ions do not diffuse freely through the luminal membranes – they must pass
through co-transporter proteins in the membrane

There are several types of these co-transporter proteins – each type transports a sodium ion
and another solute from the filtrate (eg. glucose or a particular amino acid)

Once inside the epithelial cells these solutes diffuse down their concentration gradients,
passing through transport proteins in the basal membranes (of the epithelial cells) into the
blood

Molecules reabsorbed from the proximal convoluted tubule during

selective reabsorption
All glucose in the glomerular filtrate is reabsorbed into the blood
This means no glucose should be present in the urine

Amino acids, vitamins and inorganic ions are reabsorbed

The movement of all these solutes from the proximal convoluted tubule into the capillaries
increases the water potential of the filtrate and decreases the water potential of the
blood in the capillaries
This creates a steep water potential gradient and causes water to move into the
blood by osmosis

A significant amount of urea is reabsorbed too

The concentration of urea in the filtrate is higher than in the capillaries, causing urea
to diffuse from the filtrate back into the blood

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YOUR NOTES
14. Homeostasis ⬇

Exam Tip

Selective reabsorption in the proximal convoluted tubule uses the same

method of membrane transport that moves sucrose into companion cells in
phloem tissue!
As sodium ions move passively down their concentration gradient into the
epithelial cells of the proximal convoluted tubule, this provides the energy
needed to reabsorb solute molecules (eg. glucose and amino acids) into the
epithelial cells, even against their concentration gradients.
This is known as indirect or secondary active transport, as the energy (ATP) is
used to pump sodium ions, not the solutes themselves.

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14. Homeostasis ⬇

14.1.6 OSMOREGULATION

Osmoregulation

The control of the water potential of body fluids is known as osmoregulation

Osmoregulation is a key part of homeostasis

Specialised sensory neurones, known as osmoreceptors, monitor the water potential of

the blood (these osmoreceptors are found in an area of the brain known as the
hypothalamus)

If the osmoreceptors detect a decrease in the water potential of the blood, nerve impulses
are sent along these sensory neurones to the posterior pituitary gland (another part of
the brain just below the hypothalamus)
These nerve impulses stimulate the posterior pituitary gland to release antidiuretic
hormone (ADH)

ADH molecules enter the blood and travel throughout the body

ADH causes the kidneys to reabsorb more water

This reduces the loss of water in the urine

The effect of ADH on the kidneys

Water is reabsorbed by osmosis from the filtrate in the nephron

This reabsorption occurs as the filtrate passes through structures known as collecting ducts

ADH causes the luminal membranes (ie. those facing the lumen of the nephron) of the
collecting duct cells to become more permeable to water

ADH does this by causing an increase in the number of aquaporins (water-permeable

channels) in the luminal membranes of the collecting duct cells. This occurs in the following
way:
Collecting duct cells contain vesicles, the membranes of which contain many
aquaporins

ADH molecules bind to receptor proteins, activating a signalling cascade that leads to
the phosphorylation of the aquaporin molecules

This activates the aquaporins, causing the vesicles to fuse with the luminal
membranes of the collecting duct cells

This increases the permeability of the membrane to water

As the filtrate in the nephron travels along the collecting duct, water molecules move from
the collecting duct (high water potential), through the aquaporins, and into the tissue
fluid and blood plasma in the medulla (low water potential)

As the filtrate in the collecting duct loses water it becomes more concentrated

As a result, a small volume of concentrated urine is produced. This flows from the
kidneys, through the ureters and into the bladder

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YOUR NOTES
14. Homeostasis ⬇

Exam Tip

If the water potential of the blood is too high, the exact opposite happens:
• Osmoreceptors in the hypothalamus are not stimulated
• No nerve impulses are sent to the posterior pituitary gland
• No ADH released
• Aquaporins are moved out of the luminal membranes of the collecting duct
cells
• Collecting duct cells are no longer permeable to water
• The filtrate flows along collecting duct but loses no water and is very dilute
• A large volume of dilute urine is produced
• This flows from the kidneys, through the ureters and into the bladder

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14. Homeostasis ⬇

14.1.7 THE CONTROL OF BLOOD GLUCOSE

The Control of Blood Glucose

If the concentration of glucose in the blood decreases below a certain level, cells may not
have enough glucose for respiration and may not be able to function normally

If the concentration of glucose in the blood increases above a certain level, this can also
disrupt the normal function of cells, potentially causing major problems

The control of blood glucose concentration is a key part of homeostasis

Blood glucose concentration is controlled by two hormones secreted by endocrine tissue

in the pancreas

This tissue is made up of groups of cells known as the islets of Langerhans

The islets of Langerhans contain two cell types:
α cells that secrete the hormone glucagon

β cells that secrete the hormone insulin

These α and β cells act as the receptors and initiate the response for controlling blood
glucose concentration

The control of blood glucose concentration by glucagon can be used to demonstrate the
principles of cell signalling

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14. Homeostasis ⬇

Decrease in blood glucose concentration

If a decrease in blood glucose concentration occurs, it is detected by the α and β cells in
the pancreas:
The α cells respond by secreting glucagon

The β cells respond by stopping the secretion of insulin

The decrease in blood insulin concentration reduces the use of glucose by liver and
muscle cells

Glucagon binds to receptors in the cell surface membranes of liver cells

This binding causes a conformational change in the receptor protein that activates a G
protein

This activated G protein activates the enzyme adenylyl cyclase

Active adenylyl cyclase catalyses the conversion of ATP to the second messenger, cyclic
AMP (cAMP)

cAMP binds to protein kinase A enzymes, activating them

Active protein kinase A enzymes activate phosphorylase kinase enzymes by adding

phosphate groups to them

Active phosphorylase kinase enzymes activate glycogen phosphorylase enzymes

Active glycogen phosphorylase enzymes catalyse the breakdown of glycogen to

glucose
This process is known as glycogenolysis

The enzyme cascade described above amplifies the original signal from glucagon and
results in the releasing of extra glucose by the liver to increase the blood glucose
concentration back to a normal level

Exam Tip

Make sure you know where this response to a decrease in blood glucose
concentration occurs! The enzyme cascade only occurs in liver cells, there are
no glucagon receptors on muscle cells.

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14. Homeostasis ⬇

Negative Feedback Control of Blood Glucose

Blood glucose concentration is regulated by negative feedback control mechanisms

In negative feedback systems:

Receptors detect whether a specific level is too low or too high

This information is communicated through the hormonal or nervous system to

effectors

Effectors react to counteract the change by bringing the level back to normal

In the control of blood glucose concentration:

α and β cells in the pancreas act as the receptors

They release the hormones glucagon (secreted by α cells) and insulin (secreted by
β cells)

Liver cells act as the effectors in response to glucagon and liver, muscle and fat
cells act as the effectors in response to insulin

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14. Homeostasis ⬇

14.1.8 TEST STRIPS & BIOSENSORS

Test Strips & Biosensors

Measuring urine glucose concentration
People with diabetes cannot control their blood glucose concentration so that it remains
within normal, safe limits

The presence of glucose in urine is an indicator that a person may have diabetes
If blood glucose concentration increases above a value known as the renal
threshold, not all of the glucose from the filtrate in the proximal convoluted tubule is
reabsorbed and some will be left in the urine

Test strips can be used to test urine for the presence and concentration of glucose

Two enzymes are immobilised on a small pad at one end of the test strip. These are:
glucose oxidase

peroxidase

The pad is immersed in the urine sample for a short time

If glucose is present:
Glucose oxidase catalyses a reaction in which glucose is oxidised to form gluconic
acid and hydrogen peroxide

Peroxidase then catalyses a reaction between the hydrogen peroxide and a

colourless chemical in the pad to form a brown compound and water

The colour of the pad is compared to a colour chart – different colours represent different
concentrations of glucose (the higher the concentration of glucose present, the darker the
colour)

Urine tests only show whether or not the blood glucose concentration was above the renal
threshold whilst urine was collecting in the bladder – they do not indicate the current
blood glucose concentration

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14. Homeostasis ⬇

Measuring blood glucose concentration

A biosensor can be used by people with diabetes to show their current blood glucose
concentration

Similar to the test strips, a biosensor uses glucose oxidase (but no peroxidase) immobilised
on a recognition layer

Covering the recognition layer is a partially permeable membrane that only allows small
molecules from the blood to reach the immobilised enzymes

When a small sample of blood is tested, glucose oxidase catalyses a reaction in which any
glucose in the blood sample is oxidised to form gluconic acid and hydrogen peroxide

The hydrogen peroxide produced is oxidised at an electrode that detects electron

transfers

The electron flow is proportional to the glucose concentration of the blood sample

The biosensor amplifies the current, which is then read by a processor to produce a digital
reading for blood glucose concentration

This process is complete within a matter of seconds

Exam Tip

The urine test strip will only produce a positive result for glucose. Other
sugars such as fructose, sucrose and lactose will give a negative result. This is
due to the specificity of the glucose oxidase enzyme.

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14. Homeostasis ⬇

14.2 HOMEOSTASIS IN PLANTS

14.2.1 STOMATA

Stomata

Plants carry out homeostasis – just like animals they need to maintain a constant internal
environment
For example, mesophyll cells in leaves require a constant supply of carbon
dioxide for photosynthesis

Stomata (specifically the guard cells) control the diffusion of gases in and out of leaves
This means stomata control the entry of carbon dioxide into leaves

Response of guard cells & stomata table

Regulation of stomatal aperture balances the need for carbon dioxide uptake by diffusion
with the need to minimise water loss by transpiration

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14. Homeostasis ⬇

Advantages & disadvantages of stomatal opening & closure table

Exam Tip

A stoma is actually the aperture (hole) between two guard cells, but the term
is often used to refer to the whole unit (the two guard cells and the hole
between them).
Don’t forget – stoma (singular) refers to one of these units, whereas stomata
(plural) refers to many!

Opening & Closing of Stomata

Stomata open and close in a daily rhythm

Even when the plant is kept in constant light or constant darkness, the daily
rhythm of opening and closing of the stomata continues

Opening of stomata during the day:

maintains the inward diffusion of carbon dioxide and the outward diffusion of
oxygen

allows the outward diffusion of water vapour in transpiration

Closing of stomata at night when photosynthesis cannot occur:

reduces the rate of transpiration

conserves water

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14. Homeostasis ⬇

14.2.2 GUARD CELLS

Guard Cells
Structure of guard cells
Each stoma is surrounded by two guard cells

Guard cells have the following features:

Thick cell walls facing the air outside the leaf and the stoma

Thin cell walls facing adjacent epidermal cells

Cellulose microfibrils arranged in bands around the cell

Cell walls have no plasmodesmata

Cell surface membrane is often folded and contains many channel and carrier
proteins

Cytoplasm has a high density of chloroplasts and mitochondria

Chloroplasts have thylakoids but with few grana (unlike those in mesophyll cell
chloroplasts)

Mitochondria have many cristae

Several small vacuoles rather than one large vacuole

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14. Homeostasis ⬇

Mechanism to open stomata

Guard cells open when they gain water and become turgid

Guard cells gain water by osmosis

A decrease in water potential in the guard cells is required for water to enter the cells by
osmosis

In response to light, ATP-powered proton pumps in the guard cell surface membranes

actively transport hydrogen (H+) ions out of the guard cell

This leaves the inside of the guard cells negatively charged compared to the outside

This causes channel proteins in the guard cell surface membranes to open, allowing

potassium (K+) ions to move down the electrical gradient and enter the guard cells

The potassium (K+) ions also diffuse into the guard cells down a concentration gradient
The combination of the electrical gradient and concentration gradient is known as an
electrochemical gradient

The influx of potassium (K+) ions increases the solute concentration inside the guard
cells, lowering the water potential inside the cells

Water now enters the guard cells by osmosis through aquaporins in the guard cell surface
membranes
Most of the water enters the vacuoles, causing them to increase in size

This increases the turgor pressure of the guard cells, causing the stoma to open
The bands of cellulose microfibrils only allow the guard cells to increase in length (not
diameter)

The thin outer walls of the guard cells bend more easily than thick inner walls

This causes the guard cells to become curved, opening up the stoma

Mechanism to close stomata

When certain environmental stimuli are detected (that lead to the closing of the stomata),
the proton pumps in the guard cell surface membranes stop actively transporting

hydrogen (H+) ions out of the guard cell

The potassium (K+) ions leave the guard cells

The water potential gradient is now reversed and water leaves the guard cells by
osmosis

This causes the guard cells to become flaccid, closing the stoma

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14. Homeostasis ⬇

14.2.3 ABSCISIC ACID & STOMATAL CLOSURE

Abscisic Acid & Stomatal Closure

During times of water stress, the hormone abscisic acid (ABA) is produced by plants to
stimulate the closing of their stomata
Certain environmental conditions can cause water stress, such as very high
temperatures or reduced water supplies

Guard cells have ABA receptors on their cell surface membranes

ABA binds with these receptors, inhibiting the proton pumps and therefore stopping the

active transport of hydrogen (H+) ions out of the guard cells

ABA also causes calcium (Ca2+) ions to move into the cytoplasm of the guard cells
through the cell surface membranes

The calcium ions act as second messengers:

They cause channel proteins to open that allow negatively charged ions to leave
the guard cells

This stimulates the opening of further channel proteins that allow potassium

(K+) ions to leave the guard cells

The calcium ions also stimulate the closing of channel proteins that allow

potassium (K+) ions to enter the guard cells

This loss of ions increases the water potential of the guard cells

Water leaves the guard cells by osmosis

The guard cells become flaccid, causing the stomata to close

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15. Control & Coordination ⬇

CONTENTS
15.1 Control & Coordination in Mammals
15.1.1 The Endocrine System

15.1.2 The Nervous System

15.1.3 Neurones

15.1.4 Sensory Receptor Cells

15.1.5 Sequence of Events Resulting in an Action Potential

15.1.6 Transmission of Nerve Impulses

15.1.7 Speed of Conduction of Impulses

15.1.8 The Refractory Period

15.1.9 Cholinergic Synapses

15.1.10 Stimulating Contraction in Striated Muscle

15.1.11 Ultrastructure of Striated Muscle

15.1.12 Sliding Filament Model of Muscular Contraction

15.2 Control & Coordination in Plants

15.2.1 Electrical Communication in the Venus Flytrap

15.2.2 The Role of Auxin in Elongation Growth

15.2.3 The Role of Gibberellin in Germination of Barley

15.1 CONTROL & COORDINATION IN MAMMALS

15.1.1 THE ENDOCRINE SYSTEM

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15. Control & Coordination ⬇

The Endocrine System

A hormone is a chemical substance produced by an endocrine gland and carried by the

blood
They are chemicals which transmit information from one part of the organism
to another and bring about a change

They alter the activity of one or more specific target organs

Hormones are used to control functions that do not need instant responses

The endocrine glands that produce hormones in animals are known collectively as the
endocrine system
A gland is a group of cells that produces and releases one or more substances (a
process known as secretion)

Hormones such as insulin, glucagon, ADH and adrenaline are cell-signalling

molecules that are released into the blood

Endocrine glands have a good blood supply as when they make hormones they need to get
them into the bloodstream (specifically the blood plasma) as soon as possible so they can
travel around the body to the target organs to bring about a response

Hormones only affect cells with receptors that the hormone can bind to
These are either found on the cell surface membrane, or inside cells

Receptors have to be complementary to hormones for there to be an effect

Hormones such as insulin, glucagon and ADH are peptides or small proteins
They are water-soluble and so cannot cross the phospholipid bilayer of cell
surface membranes

These hormones bind to receptors on the cell surface membranes of their target cells,
which activates second messengers to transfer the signal throughout the cytoplasm

Hormones such as testosterone, oestrogen and progesterone are steroid hormones

They are lipid-soluble and so can cross the phospholipid bilayer

These hormones bind to receptors in the cytoplasm or nucleus of their target cells

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15. Control & Coordination ⬇

15.1.2 THE NERVOUS SYSTEM

The Nervous System

The human nervous system consists of the:

Central nervous system (CNS) – the brain and the spinal cord

Peripheral nervous system (PNS) – all of the nerves in the body

It allows us to make sense of our surroundings and respond to them and to coordinate and
regulate body functions

Information is sent through the nervous system as nerve impulses – electrical signals that
pass along nerve cells known as neurones

A bundle of neurones is known as a nerve

Neurones coordinate the activities of sensory receptors (eg. those in the eye), decision-
making centres in the central nervous system, and effectors such as muscles and
glands

The nervous system & the endocrine system table

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15. Control & Coordination ⬇

15.1.3 NEURONES

Neurones

Neurones have a long fibre known as an axon

The axon is insulated by a fatty sheath with small uninsulated sections along its length
(called nodes of Ranvier)
The sheath is made of myelin, a substance made by specialised cells known as
Schwann cells

Myelin is made when Schwann cells wrap themselves around the axon along its length

This means that the electrical impulse does not travel down the whole axon, but jumps from
one node to the next
This means that less time is wasted transferring the impulse from one cell to another

Their cell bodies contain many extensions called dendrites

This means they can connect to many other neurones and receive impulses from them,
forming a network for easy communication

An example of a neurone

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15. Control & Coordination ⬇

There are three main types of neurone: sensory, relay and motor
Sensory neurones carry impulses from receptors to the CNS (brain or spinal cord)

Relay (intermediate) neurones are found entirely within the CNS and connect
sensory and motor neurones

Motor neurones carry impulses from the CNS to effectors (muscles or glands)

The three types of neurone – the red line shows the direction of impulses

Each type of neurone has a slightly different structure

Motor neurones have:

A large cell body at one end, that lies within the spinal cord or brain

A nucleus that is always in its cell body

Many highly-branched dendrites that extend from the cell body, providing a large
surface area for the axon terminals of other neurones

Sensory neurones have the same basic structure as motor neurones, but have:
One long axon with a cell body that branches off in the middle of the axon – it may be
near the source of stimuli or in a swelling of a spinal nerve known as a ganglion

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15. Control & Coordination ⬇

Reflex arc
Sensory neurones, relay (intermediate) neurones and motor neurones work together to
bring about a response to a stimulus

A reflex arc is a pathway along which impulses are transmitted from a receptor to an
effector without involving ‘conscious’ regions of the brain

As it does not involve the brain, a reflex response is quicker than any other type of nervous
response

Examples of simple reflex actions that are coordinated by these pathways are:
Removing the hand rapidly from a sharp or hot object

Blinking

Focusing of the eye on an object

Controlling how much light enters the eye

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YOUR NOTES
15. Control & Coordination ⬇

How sensory neurones, intermediate (relay) neurones and motor neurones work together
to carry out a reflex action

In the example above:

A pin (the stimulus) is detected by a pain receptor in the skin

The sensory neurone sends electrical impulses to the spinal cord (the
coordinator)

Electrical impulses are passed on to relay neurone in the spinal cord

The relay neurone connects to the motor neurone and passes the impulses on

The motor neurone carries the impulses to the muscle in the leg (the effector)

The impulses cause the muscle to contract and pull the leg up and away from the
sharp object (the response)

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15. Control & Coordination ⬇

The pathway of a reflex arc

Exam Tip

You may be asked to identify the different types of neurones in a diagram. It

can be helpful to memorise the key differences between them – such as the
location and size of the cell body.

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15. Control & Coordination ⬇

15.1.4 SENSORY RECEPTOR CELLS

Sensory Receptor Cells

A cell that responds to a stimulus is called a receptor cell

Receptor cells are transducers – they convert energy in one form (such as light, heat or
sound) into energy in an electrical impulse within a sensory neurone

Receptor cells are often found in sense organs (eg. light receptor cells are found in the eye)
Some receptors, such as light receptors in the eye and chemoreceptors in the taste
buds, are specialised cells that detect a specific type of stimulus and influence the
electrical activity of a sensory neurone

Other receptors, such as some kinds of touch receptors, are just the ends of the
sensory neurones themselves

When receptors cells are stimulated they are depolarised

If the stimulus is very weak, the cells are not sufficiently depolarised and the
sensory neurone is not activated to send impulses

If the stimulus is strong enough, the sensory neurone is activated and transmits
impulses to the CNS

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15. Control & Coordination ⬇

15.1.5 SEQUENCE OF EVENTS RESULTING IN AN ACTION

POTENTIAL

Sequence of Events Resulting in an Action Potential

The surface of the tongue is covered in many small bumps known as papillae

The surface of each papilla is covered in many taste buds

Each taste bud contains many receptor cells known as chemoreceptors

These chemoreceptors are sensitive to chemicals in food and drinks

Each chemoreceptor is covered with receptor proteins

Different receptor proteins detect different chemicals

An example of the sequence of events that results in an action

potential in a sensory neurone
Chemoreceptors in the taste buds that detect salt (sodium chloride) respond directly to
sodium ions

If salt is present in the food (dissolved in saliva) being eaten or the liquid being drunk:
Sodium ions diffuse through highly selective channel proteins in the cell surface
membranes of the microvilli of the chemoreceptor cells

This leads to depolarisation of the chemoreceptor cell membrane

The increase in positive charge inside the cell is known as the receptor potential

If there is sufficient stimulation by sodium ions and sufficient depolarisation of the

membrane, the receptor potential becomes large enough to stimulate voltage-gated
calcium ion channel proteins to open

As a result, calcium ions enter the cytoplasm of the chemoreceptor cell and
stimulate exocytosis of vesicles containing neurotransmitter from the basal
membrane of the chemoreceptor

The neurotransmitter stimulates an action potential in the sensory neurone

The sensory neurone then transmits an impulse to the brain

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15. Control & Coordination ⬇

When receptors (such as chemoreceptors) are stimulated, they are depolarised

If the stimulus is very weak or below a certain threshold, the receptor cells won’t be
sufficiently depolarised and the sensory neurone will not be activated to send impulses

If the stimulus is strong enough to increase the receptor potential above the threshold
potential then the receptor will stimulate the sensory neurone to send impulses

This is an example of the all-or-none law

An impulse is only transmitted if the initial stimulus is sufficient to increase the
membrane potential above a threshold potential

Rather than staying constant, threshold levels in receptors often increase with
continued stimulation, so that a greater stimulus is required before impulses are sent
along sensory neurones

Exam Tip

Some receptors, like the chemoreceptors described above, are specialised

cells that detect a specific type of stimulus and affect the sensory
neurone’s electrical activity. Other receptors are just the ends of the
sensory neurones (for example, many types of touch receptors).

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YOUR NOTES
15. Control & Coordination ⬇

15.1.6 TRANSMISSION OF NERVE IMPULSES

Transmission of Nerve Impulses

Neurones transmit electrical impulses, which travel extremely quickly along the neurone
cell surface membrane from one end of the neurone to the other

Unlike a normal electric current, these impulses are not a flow of electrons

These impulses, known as action potentials, occur via very brief changes in the
distribution of electrical charge across the cell surface membrane
Action potentials are caused by the rapid movement of sodium ions and
potassium ions across the membrane of the axon

Resting potential
In a resting axon (one that is not transmitting impulses), the inside of the axon always
has a slightly negative electrical potential compared to outside the axon

This potential difference is usually about -70mV (ie. the inside of the axon has an
electrical potential about 70mV lower than the outside)

This is called the resting potential

Several factors contribute to maintaining the resting potential:

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15. Control & Coordination ⬇

How the resting potential is maintained table

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15. Control & Coordination ⬇

Action potentials
There are channel proteins in the axon membrane that allow sodium ions or potassium
ions to pass through

These open and close depending on the electrical potential (or voltage) across the
axon membrane and are known as voltage-gated channel proteins (they are closed
when the axon membrane is at its resting potential)

When an action potential is stimulated (eg. by a receptor cell) in a neurone, the following
steps occur:
Voltage-gated channel proteins in the axon membrane open

Sodium ions pass into the axon down the electrochemical gradient (there is a
greater concentration of sodium ions outside the axon than inside. The inside of the
axon is negatively charged, attracting the positively charged sodium ions)

This reduces the potential difference across the axon membrane as the inside of
the axon becomes less negative – a process known as depolarisation

This triggers more channels to open, allowing more sodium ions to enter and
causing more depolarisation

This is an example of positive feedback (a small initial depolarisation leads to

greater and greater levels of depolarisation)

If the potential difference reaches around -50mV (known as the threshold value),
many more channels open and many more sodium ions enter causing the
inside of the axon to reach a potential of around +30mV

An action potential is generated

The depolarisation of the membrane at the site of the first action potential causes
current to flow to the next section of the axon membrane, depolarising it and
causing sodium ion voltage-gated channel proteins to open

This triggers the production of another action potential in this section of the axon
membrane and the process continues

In the body, this allows action potentials to begin at one end of an axon and then pass
along the entire length of the axon membrane

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15. Control & Coordination ⬇

Repolarisation and the refractory period

Very shortly (about 1 ms) after an action potential in a section of axon membrane is
generated, all the sodium ion voltage-gated channel proteins in this section close,
stopping any further sodium ions diffusing into the axon

Potassium ion voltage-gated channel proteins in this section of axon membrane now
open, allowing the diffusion of potassium ions out of the axon, down their concentration
gradient

This returns the potential difference to normal (about -70mV) – a process known as
repolarisation
There is actually a short period of hyperpolarisation. This is when the potential
difference across this section of axon membrane briefly becomes more negative
than the normal resting potential

The potassium ion voltage-gated channel proteins then close and the sodium ion channel
proteins in this section of membrane become responsive to depolarisation again
Until this occurs, this section of the axon membrane is in a period of recovery and is
unresponsive

This is known as the refractory period

Exam Tip

During the refractory period, a section of the axon is unresponsive. This is

very important as it ensures that ‘new’ action potentials are generated ahead
(ie. further along the axon), rather than behind the original action potential.
This makes the action potentials discrete events and means the impulse can
only travel in one direction. This is essential for the successful and efficient
transmission of nerve impulses along neurones.

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15. Control & Coordination ⬇

15.1.7 SPEED OF CONDUCTION OF IMPULSES

Speed of Conduction of Impulses

The speed of conduction of an impulse refers to how quickly the impulse is

transmitted along a neurone

It is determined by two main factors:

the presence or absence of myelin (ie. whether or not the axon is insulated by a
myelin sheath)

the diameter of the axon

Myelination
In unmyelinated neurones, the speed of conduction is very slow

By insulating the axon membrane, the presence of myelin increases the speed at which
action potentials can travel along the neurone:
In sections of the axon that are surrounded by a myelin sheath, depolarisation (and
the action potentials that this would lead to) cannot occur, as the myelin sheath
stops the diffusion of sodium ions and potassium ions

Action potentials can only occur at the nodes of Ranvier (small uninsulated sections
of the axon)

The local circuits of current that trigger depolarisation in the next section of the axon
membrane exist between the nodes of Ranvier

This means the action potentials ‘jump’ from one node to the next

This is known as saltatory conduction

This allows the impulse to travel much faster (up to 50 times faster) than in an
unmyelinated axon of the same diameter

Diameter
The speed of conduction of an impulse along neurones with thicker axons is greater than
along those with thinner ones

Thicker axons have an axon membrane with a greater surface area over which diffusion
of ions can occur

This increases the rate of diffusion of sodium ions and potassium ions, which in turn
increases the rate at which depolarisation and action potentials can occur

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15. Control & Coordination ⬇

15.1.8 THE REFRACTORY PERIOD

The Refractory Period

Very shortly (about 1 ms) after an action potential has been generated in a section of the
axon membrane, all the sodium ion voltage-gated channel proteins in this section
close. This stops any further sodium ions diffusing into the axon

Potassium ion voltage-gated channel proteins in this section of axon membrane open,
allowing the diffusion of potassium ions out of the axon, down their concentration gradient

This gradually returns the potential difference to normal (about -70mV) – a process
known as repolarisation

Once the resting potential is close to being reestablished, the potassium ion voltage-gated
channel proteins close and the sodium ion channel proteins in this section of membrane
become responsive to depolarisation again

Until this occurs, this section of the axon membrane is in a period of recovery and is
unresponsive

This is known as the refractory period

The importance of the refractory period

The refractory period is important for the following reasons:
It ensures that action potentials are discrete events, stopping them from merging
into one another

It ensures that ‘new’ action potentials are generated ahead (ie. further along the
axon), rather than behind the original action potential, as the region behind is
‘recovering’ from the action potential that has just occurred

This means that the impulse can only travel in one direction, which is essential for
the successful and efficient transmission of nerve impulses along neurones

This also means there is a minimum time between action potentials occurring at
any one place along a neurone

The length of the refractory period is key in determining the maximum

frequency at which impulses can be transmitted along neurones (between 500 and
1000 per second)

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15. Control & Coordination ⬇

15.1.9 CHOLINERGIC SYNAPSES

Cholinergic Synapses

Where two neurones meet, they do not actually come into physical contact with each other –
a very small gap, known as the synaptic cleft, separates them

The ends of the two neurones, along with the synaptic cleft, form a synapse

A synapse

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15. Control & Coordination ⬇

Synaptic transmission – basic mechanism

Electrical impulses cannot ‘jump’ across synapses

When an electrical impulse arrives at the end of the axon on the presynaptic neurone,
chemical messengers called neurotransmitters are released from vesicles at the
presynaptic membrane

The neurotransmitters diffuse across the synaptic cleft and temporarily bind with
receptor molecules on the postsynaptic membrane

This stimulates the postsynaptic neurone to generate an electrical impulse that then
travels down the axon of the postsynaptic neurone

The neurotransmitters are then destroyed or recycled to prevent continued stimulation of

the second neurone, which could cause repeated impulses to be sent

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15. Control & Coordination ⬇

The basic mechanism of synaptic transmission

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15. Control & Coordination ⬇

Synaptic transmission – detailed mechanism

There are over 40 different known neurotransmitters

One of the key neurotransmitters used throughout the nervous system is acetylcholine
(ACh)

Synapses that use the neurotransmitter ACh are known as cholinergic synapses

The detailed process of synaptic transmission using ACh is as follows:

The arrival of an action potential at the presynaptic membrane causes
depolarisation of the membrane

This stimulates voltage-gated calcium ion channel proteins to open

Calcium ions diffuse down an electrochemical gradient from the tissue fluid
surrounding the synapse (high concentration of calcium ions) into the cytoplasm of
the presynaptic neurone (low concentration of calcium ions)

This stimulates ACh-containing vesicles to fuse with the presynaptic

membrane, releasing ACh molecules into the synaptic cleft

The ACh molecules diffuse across the synaptic cleft and temporarily bind to
receptor proteins in the postsynaptic membrane

This causes a conformational change in the receptor proteins, which then open,
allowing sodium ions to diffuse down an electrochemical gradient into the
cytoplasm of the postsynaptic neurone

The sodium ions cause depolarisation of the postsynaptic membrane, re-

starting the electrical impulse (that can now continue down the axon of the
postsynaptic neurone)

To prevent the sodium ion channels staying permanently open and to stop permanent
depolarisation of the postsynaptic membrane, the ACh molecules are broken
down and recycled

The enzyme acetylcholinesterase catalyses the hydrolysis of the ACh molecules

into acetate and choline

The choline is absorbed back into the presynaptic membrane and reacts with
acetyl coenzyme A to form ACh, which is then packaged into presynaptic vesicles
ready to be used when another action potential arrives

This entire sequence of events takes 5 – 10 ms

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15. Control & Coordination ⬇

15.1.10 STIMULATING CONTRACTION IN STRIATED MUSCLE

Stimulating Contraction in Striated Muscle

Striated muscle contracts when it receives an impulse from a motor neurone via the
neuromuscular junction

When an impulse travelling along the axon of a motor neurone arrives at the presynaptic
membrane, the action potential causes calcium ions to diffuse into the neurone

This stimulates vesicles containing the neurotransmitter acetylcholine (ACh) to fuse with
the presynaptic membrane

The ACh that is released diffuses across the neuromuscular junction and binds to receptor
proteins on the sarcolemma (surface membrane of the muscle fibre cell)
This stimulates ion channels in the sarcolemma to open, allowing sodium ions to diffuse
in

This depolarises the sarcolemma, generating an action potential that passes down the
T-tubules towards the centre of the muscle fibre

These action potentials cause voltage-gated calcium ion channel proteins in the
membranes of the sarcoplasmic reticulum (which lie very close to the T-tubules) to open

Calcium ions diffuse out of the sarcoplasmic reticulum (SR) and into the sarcoplasm
surrounding the myofibrils

Calcium ions bind to troponin molecules, stimulating them to change shape

This causes the troponin and tropomyosin proteins to change position on the thin (actin)
filaments

The myosin-binding sites are exposed on the actin molecules

The process of muscle contraction (known as the sliding filament model) can now begin

Exam Tip

You may have noticed that there are a lot of similarities between the events
at the neuromuscular junction and those that occur at cholinergic synapses. A
cholinergic synapse is between two neurones, a neuromuscular junction is
between a neurone and muscle. Make sure you understand the similarities
and differences and don’t get confused between the two.

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15. Control & Coordination ⬇

15.1.11 ULTRASTRUCTURE OF STRIATED MUSCLE

Ultrastructure of Striated Muscle

Striated muscle makes up the muscles in the body that are attached to the skeleton

Striated muscle is made up of muscle fibres

A muscle fibre is a highly specialised cell-like unit:

Each muscle fibre contains an organised arrangement of contractile proteins in the
cytoplasm

Each muscle fibre is surrounded by a cell surface membrane

Each muscle fibre contains many nuclei – this is why muscle fibres are not usually
referred to as cells

The different parts of a muscle fibre have different names to the equivalent parts of a normal
cell:
Cell surface membrane = sarcolemma

Cytoplasm = sarcoplasm

Endoplasmic reticulum = sarcoplasmic reticulum (SR)

The sarcolemma has many deep tube-like projections that fold in from its outer surface:
These are known as transverse system tubules or T-tubules

These run close to the SR

The sarcoplasm contains mitochondria and myofibrils

The mitochondria carry out aerobic respiration to generate the ATP required for
muscle contraction

Myofibrils are bundles of actin and myosin filaments, which slide past each other
during muscle contraction

The membranes of the SR contain protein pumps that transport calcium ions into the
lumen of the SR

Myofibrils
Myofibrils are located in the sarcoplasm

Each myofibril is made up of two types of protein filament:

Thick filaments made of myosin

Thin filaments made of actin

These two types of filament are arranged in a particular order, creating different types of
bands and line

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15. Control & Coordination ⬇

Myofibrils parts & descriptions table

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15. Control & Coordination ⬇

15.1.12 SLIDING FILAMENT MODEL OF MUSCULAR CONTRACTION

Sliding Filament Model of Muscular Contraction

Structure of thick & thin filaments in a myofibril
The thick filaments within a myofibril are made up of myosin molecules
These are fibrous protein molecules with a globular head

The fibrous part of the myosin molecule anchors the molecule into the thick
filament

In the thick filament, many myosin molecules lie next to each other with their
globular heads all pointing away from the M line

The thin filaments within a myofibril are made up of actin molecules

These are globular protein molecules

Many actin molecules link together to form a chain

Two actin chains twist together to form one thin filament

A fibrous protein known as tropomyosin is twisted around the two actin chains

Another protein known as troponin is attached to the actin chains at regular intervals

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15. Control & Coordination ⬇

How muscles contract – the sliding filament model

Muscles cause movement by contracting

During muscle contraction, sarcomeres within myofibrils shorten as the Z discs are
pulled closer together

This is known as the sliding filament model of muscle contraction and occurs via the
following process:
An action potential arrives at the neuromuscular junction

Calcium ions are released from the sarcoplasmic reticulum (SR)

Calcium ions bind to troponin molecules, stimulating them to change shape

This causes troponin and tropomyosin proteins to change position on the actin
(thin) filaments

Myosin binding sites are exposed on the actin molecules

The globular heads of the myosin molecules bind with these sites, forming
cross-bridges between the two types of filament

The myosin heads move and pull the actin filaments towards the centre of
the sarcomere, causing the muscle to contract a very small distance

ATP hydrolysis occurs at the myosin heads, providing the energy required for the
myosin heads to release the actin filaments

The myosin heads move back to their original positions and bind to new binding
sites on the actin filaments, closer to the Z disc

The myosin heads move again, pulling the actin filaments even closer the centre of
the sarcomere, causing the sarcomere to shorten once more and pulling the Z
discs closer together

The myosin heads hydrolyse ATP once more in order to detach again

As long as troponin and tropomyosin are not blocking the myosin-binding sites and
the muscle has a supply of ATP, this process repeats until the muscle is fully
contracted

Exam Tip

The sliding filament model can be difficult to visualise fully with diagrams. To
help you more clearly understand the steps involved, try to find some
animations or videos of the sliding filament model online to see the
movement of the myosin heads and thin (actin) filaments during muscle
contraction!

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15. Control & Coordination ⬇

15.2 CONTROL & COORDINATION IN PLANTS

15.2.1 ELECTRICAL COMMUNICATION IN THE VENUS FLYTRAP

Electrical Communication in the Venus Flytrap

Plants possess communication systems that enable them to coordinate the different parts
of their bodies

The Venus flytrap is a carnivorous plant that gets its supply of nitrogen compounds by
trapping and digesting small animals (mainly insects)

The specialised leaf is divided into two lobes either side of a midrib

The inside of the lobes is red and has nectar-secreting glands on the edges to attract
insects

Each lobe has three stiff sensory hairs that respond to being touched

If an insect (eg. a fly) touches one of these hairs with enough force, action potentials are
stimulated, which then travel very fast across the leaf

These action potentials cause the two lobes to fold together along the midrib, capturing the
insect

How the closure of the trap is achieved

If one of the sensory hairs is touched with enough force, calcium ion channels in cells at
the base of the hair are activated

When these channels open, calcium ions flow in and generate a receptor potential

If two of the sensory hairs are stimulated within a period of about 30 seconds, or one hair is
stimulated twice within this period, action potentials will travel across the trap and cause it
to close
When the trap is open the lobes of the leaf are convex in shape but when the trap is
triggered, the lobes quickly become concave, bending downwards and causing the
trap to shut – it is thought this occurs as a result of a release of elastic tension in the
cell walls

Sealing the trap requires ongoing activation of the sensory hairs – the prey trapped inside
provides this ongoing stimulation, generating further action potentials

Further stimulation of the sensory hairs stimulate calcium ions to enter gland cells where
they stimulate the exocytosis of vesicles containing digestive enzymes

The trap then stays shut for up to a week to allow the prey to be digested and the nutrients
from it to be absorbed by the plant

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15. Control & Coordination ⬇

15.2.2 THE ROLE OF AUXIN IN ELONGATION GROWTH

The Role of Auxin in Elongation Growth

Plant hormones (also known as plant growth regulators) are responsible for most
communication within plants

Auxins are a type of plant growth regulator that influence many aspects of growth, including
elongation growth which determines the overall length of roots and shoots

The principle chemical in the group of auxins made by plants is IAA (indole 3-acetic acid) and
this chemical is often simply referred to as ‘auxin’

Auxin (IAA) is synthesised in the growing tips of roots and shoots (ie. in the
meristems, where cells are dividing)
Growth in these meristems occurs in three stages:
cell division by mitosis

cell elongation by absorption of water

cell differentiation

Auxin (IAA) is involved in controlling growth by elongation

Controlling growth by elongation

Auxin molecules bind to a receptor protein on the cell surface membrane

Auxin stimulates ATPase proton pumps to pump hydrogen ions from the cytoplasm into
the cell wall (across the cell surface membrane)

This acidifies the cell wall (lowers the pH of the cell wall)

This activates proteins known as expansins, which loosen the bonds between cellulose
microfibrils

At the same time, potassium ion channels are stimulated to open

This leads to an increase in potassium ion concentration in the cytoplasm, which

decreases the water potential of the cytoplasm

This causes the cell to absorb water by osmosis (water enters the cell through
aquaporins)

This increases the internal pressure of the cell, causing the cell wall to stretch (made
possible by expansin proteins)

The cell elongates

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15. Control & Coordination ⬇

15.2.3 THE ROLE OF GIBBERELLIN IN GERMINATION OF BARLEY

The Role of Gibberellin in Germination of Barley

Gibberellins are a type of plant growth regulator involved in controlling seed germination
and stem elongation

When a barley seed is shed from the parent plant, it is in a state of dormancy (contains very
little water and is metabolically inactive)

This allows the seed to survive harsh conditions until the conditions are right for successful
germination (eg. the seed can survive a cold winter until temperatures rise again in spring)

The barley seed contains:

An embryo – will grow into the new plant when the seed germinates
An endosperm – a starch-containing energy store surrounding the embryo

An aleurone layer – a protein-rich layer on the outer edge of the endosperm

When the conditions are right, the barley seed starts to absorb water to begin the process
of germination

This stimulates the embryo to produce gibberellins

Gibberellin molecules diffuse into the aleurone layer and stimulate the cells there to
synthesise amylase
In barley seeds, it has been shown that gibberellin does this by regulating genes
involved in the synthesis of amylase, causing an increase in the transcription
of mRNA coding for amylase

The amylase hydrolyses starch molecules in the endosperm, producing soluble maltose
molecules

The maltose is converted to glucose and transported to the embryo

This glucose can be respired by the embryo, providing the embryo with the energy needed
for it to grow

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16. Inheritance ⬇

CONTENTS
16.1 Passage of Information from Parents to Offspring
16.1.1 Haploidy & Diploidy

16.1.2 Homologous Chromosomes

16.1.3 Meiosis in Animal & Plant Cells

16.1.4 Identifying the Stages of Mieosis

16.1.5 Meiosis: Sources of Genetic Variation

16.2 The Roles of Genes in Determining the Phenotype

16.2.1 Key Terms in Genetics

16.2.2 Predicting Inheritance: Monohybrid Crosses

16.2.3 Predicting Inheritance: Dihybrid Crosses

16.2.4 Predicting Inheritance: Test Crosses

16.2.5 Predicting Inheritance: Chi-squared Test

16.2.6 Genes, Proteins & Phenotype

16.2.7 The Role of Gibberellin in Stem Elongation

16.3 Gene Control

16.3.1 Gene Control

16.3.2 Gene Control: Lac Operon

16.3.3 Gene Control: Transcription Factors

16.1 PASSAGE OF INFORMATION FROM PARENTS TO

OFFSPRING

16.1.1 HAPLOIDY & DIPLOIDY

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Haploid & Diploid Cells

A diploid cell is a cell that contains two complete sets of chromosomes (2n)
These chromosomes contain the DNA necessary for protein synthesis and cell function

Nearly all cells in the human body are diploid with 23 pairs (46) of chromosomes in
their nucleus

Haploid cells contain one complete set of chromosomes (n)

In other words they have half the number of chromosomes compared to diploid cells

Humans have haploid cells that contain 23 chromosomes in their nucleus

These haploid cells are called gametes and they are involved in sexual reproduction

For humans they are the female egg and the male sperm

Haploidy and diploidy are terms that can be applied to cells across different species
They describe the number of sets of chromosomes, not the total number of
chromosomes

Exam Tip

Red blood cells are an exception when it comes to chromosome number as

they don’t have a nucleus!
You may be asked to estimate the number of chromosomes that would be
present in the haploid cell of a species. For example, dogs have 78
chromosomes in their diploid cells. When trying to find the number of
chromosomes in their haploid cells simply remember that diploid is 2n and
haploid is n, meaning you just need to divide the number of chromosomes
by 2. So dogs have 39 chromosomes in their haploid cells!

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The Need for Reduction Division during Meiosis

During fertilization the nuclei of gametes fuse together to form the nucleus of the
zygote

Both gametes must contain the correct number of chromosomes in order for the zygote to be
viable. If a zygote has too many or too few chromosomes it may not survive

For a diploid zygote this means that the gametes must be haploid
n + n = 2n

Meiosis produces haploid gametes during sexual reproduction

The first cell division of meiosis is a reduction division

This is a nuclear division that reduces the chromosome number of a cell

In humans the chromosome number is reduced from 46 (diploid) to 23 (haploid)

The reduction in chromosome number during meiosis ensures the gametes formed are
haploid

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16.1.2 HOMOLOGOUS CHROMOSOMES

Homologous Chromosomes

In diploid cells there are two complete sets of chromosomes in the nucleus

Chromosones have a characteristic shape

They have a fixed length

The position of the centromere is in a particular location

These characteristic features allow for each chromosome to be identified in a

photomicrograph

In photomicrographs chromosomes are often grouped into their homologous pairs

Homologous chromosomes:
Carry the same genes in the same positions

Are the same shape

During fertilization a diploid zygote is formed

In a zygote one chromosome of each homologous pair comes from the female gamete
and the other comes from the male gamete

Having the same genes in the same order helps homologous chromosomes line up alongside
each other during meiosis

Exam Tip

Although homologous pairs of chromosomes contain the same genes in the

same order they don’t necessarily carry the same alleles (form) of each gene!

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16.1.3 MEIOSIS IN ANIMAL & PLANT CELLS

Meiosis in Animal & Plant Cells

Meiosis is a form of nuclear division that results in the production of haploid cells from
diploid cells

It produces gametes in plants and animals that are used in sexual reproduction

It has many similarities to mitosis however it has two divisions: meiosis I and meiosis II

Within each division there are the following stages: prophase, metaphase, anaphase and
telophase

Prophase I
DNA condenses and becomes visible as chromosomes

DNA replication has already occurred so each chromosome consists of two sister
chromatids joined together by a centromere

The chromosomes are arranged side by side in homologous pairs

A pair of homologous chromosomes is called a bivalent

As the homologous chromosomes are very close together the crossing over of non-sister
chromatids may occur. The point at which the crossing over occurs is called the chiasma
(chiasmata; plural)

In this stage centrioles migrate to opposite poles and the spindle is formed

The nuclear envelope breaks down and the nucleolus disintegrates

Metaphase I
The bivalents line up along the equator of the spindle, with the spindle fibres attached
to the centromeres

Anaphase I
The homologous pairs of chromosomes are separated as microtubules pull whole
chromosomes to opposite ends of the spindle

The centromeres do not divide

Telophase I
The chromosomes arrive at opposite poles

Spindle fibres start to break down

Nuclear envelopes form around the two groups of chromosomes and nucleoli reform

Some plant cells go straight into meiosis II without reformation of the nucleus in telophase I

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Cytokinesis
This is when the division of the cytoplasm occurs

Cell organelles also get distributed between the two developing cells

In animal cells: the cell surface membrane pinches inwards creating a cleavage furrow in
the middle of the cell which contracts, dividing the cytoplasm in half

In plant cells, vesicles from the Golgi apparatus gather along the equator of the spindle (the
cell plate). The vesicles merge with each other to form the new cell surface membrane
and also secrete a layer of calcium pectate which becomes the middle lamella. Layers of
cellulose are laid upon the middle lamella to form the primary and secondary walls of the cell

The end product of cytokinesis in meiosis I is two complete haploid cells

Second division of Meiosis : Meiosis II

There is no interphase between meiosis I and meiosis II so the DNA is not replicated

The second division of meiosis is almost identical to the stages of mitosis

Prophase II
The nuclear envelope breaks down and chromosomes condense

A spindle forms at a right angle to the old one

Metaphase II
Chromosomes line up in a single file along the equator of the spindle

Anaphase II
Centromeres divide and individual chromatids are pulled to opposite poles

This creates four groups of chromosomes that have half the number of
chromosomes compared to the original parent cell

Telophase II
Nuclear membranes form around each group of chromosomes

Cytokinesis
Cytoplasm divides as new cell surface membranes are formed creating four
haploid cells

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Exam Tip

Understanding the difference between chromosomes and chromatids can be

difficult. We count chromosomes by the number of centromeres present.
So when the 46 chromosomes duplicate during interphase and the amount
of DNA in the cell doubles there are still only 46 chromosomes present
because there are still only 46 centromeres present. However, there are now
92 chromatids, which are strands of replicated chromosomes.

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16.1.4 IDENTIFYING THE STAGES OF MIEOSIS

Identifying the Stages of Meiosis

Cells undergoing meiosis can be observed and photographed using specialised microscopes

The different stages of meiosis have distinctive characteristics meaning they can be
identified from photomicrographs or diagrams

Meiosis I or Meiosis II
Homologous chromosomes pair up side by side in meiosis I only

This means if there are pairs of chromosomes in a diagram or photomicrograph meiosis I

must be occurring
The number of cells forming can help distinguish between meiosis I and II

If there are two new cells forming it is meiosis I but if there are four new cells forming it
is meiosis II

The distinguishing features at each stage of Meiosis I

Prophase I: Homologous pairs of chromosomes are visible

Metaphase I: Homologous pairs are lined up side by side along the equator of spindle

Anaphase I: Whole chromosomes are being pulled to opposite poles with centromeres
intact

Telophase I: There are 2 groups of condensed chromosomes around which nuclei

membranes are forming

Cytokinesis: Cytoplasm is dividing and cell membrane is pinching inwards to form two
cells

The distinguishing features at each stage of Meiosis II

Prophase II: Single whole chromosomes are visible

Metaphase II: Single whole chromosomes are lined up along the equator of the spindle in
single file (at 90 degree angle to the old spindle)

Anaphase II: Centromeres divide and chromatids are being pulled to opposite poles

Telophase II: Nuclei are forming around the 4 groups of condensed chromosomes

Cytokinesis: Cytoplasm is dividing and four haploid cells are forming

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Identifying the stages of meiosis table

Exam Tip

For metaphase remember M for the middle of the spindle and cell which is
where the chromosomes will be lined up.
For anaphase remember A for away from the middle to the poles, which is
where the chromosomes / chromatids are being pulled.

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16.1.5 MEIOSIS: SOURCES OF GENETIC VARIATION

Meiosis: Sources of Genetic Variation

Having genetically different offspring can be advantageous for natural selection

Meiosis has several mechanisms that increase the genetic diversity of gametes
produced

Both crossing over and independent assortment (random orientation) result in different
combinations of alleles in gametes

Crossing over
Crossing over is the process by which non-sister chromatids exchange alleles
Process:
During meiosis I homologous chromosomes pair up and are in very close proximity to
each other

The non-sister chromatids can cross over and get entangled

These crossing points are called chiasmata

The entanglement places stress on the DNA molecules

As a result of this a section of chromatid from one chromosome may break and
rejoin with the chromatid from the other chromosome

This swapping of alleles is significant as it can result in a new combination of alleles on

the two chromosomes

There is usually at least one, if not more, chiasmata present in each bivalent during meiosis

Crossing over is more likely to occur further down the chromosome away from the
centromere

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Independent assortment
Independent assortment is the production of different combinations of alleles in
daughter cells due to the random alignment of homologous pairs along the equator
of the spindle during metaphase I

The different combinations of chromosomes in daughter cells increases genetic variation

between gametes

In prophase I homologous chromosomes pair up and in metaphase I they are pulled towards
the equator of the spindle
Each pair can be arranged with either chromosome on top, this is completely
random

The orientation of one homologous pair is independent / unaffected by the

orientation of any other pair

The homologous chromosomes are then separated and pulled apart to different poles

The combination of alleles that end up in each daughter cell depends on how the pairs of
homologous chromosomes were lined up

To work out the number of different possible chromosome combinations the formula 2n can
be used, where n corresponds to the number of chromosomes in a haploid cell

For humans this is 223 which calculates as 8 324 608 different combinations

Exam Tip

Several sources of genetic variation have been outlined above. It is also worth
remembering that genetic variation can occur on an even smaller scale than
chromosomes. Mutations can occur within genes. A random mutation that
takes place during DNA replication can lead to the production of new alleles
and increased genetic variation.

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Fusion of Gametes

Meiosis creates genetic variation between the gametes produced by an individual

through crossing over and independent assortment

This means each gamete carries substantially different alleles

During fertilization any male gamete can fuse with any female gamete to form a zygote

This random fusion of gametes at fertilization creates genetic variation between zygotes
as each will have a unique combination of alleles

There is an almost zero chance of individual organisms resulting from successive sexual
reproduction being genetically identical

Exam Tip

These sources of genetic variation explain why relatives can differ so much
from each other. Even with the same parents, individuals can be genetically
distinct due to the processes outlined above.

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16.2 THE ROLES OF GENES IN DETERMINING THE

PHENOTYPE

16.2.1 KEY TERMS IN GENETICS

Key Terms in Genetics

Genes & alleles
The DNA contained within chromosomes is essential for cell survival

Every chromosome consists of a long DNA molecule which codes for several different
proteins

A length of DNA that codes for a single polypeptide or protein is called a gene

The position of a gene on a chromosome is its locus (plural: loci)

Each gene can exist in two or more different forms called alleles

Different alleles of a gene have slightly different nucleotide sequences but they still
occupy the same position (locus) on the chromosome

Example of alleles
One of the genes for coat colour in horses is Agouti

This gene for coat colour is found on the same position on the same chromosome for all
horses

Hypothetically there are two different forms (alleles) of that gene found in horses: A and a

Each allele can produce a different coat colour:

Allele A → black coat

Allele a → chestnut coat

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Genotype & phenotype

The chromosomes of eukaryotic cells occur in homologous pairs (there are two copies of
each chromosome)

As a result cells have two copies of every gene

As there are two copies of a gene present in an individual that means there can be different
allele combinations within an individual

The genotype of an organism refers to the alleles of a gene possessed by that individual.
The different alleles can be represented by letters

When the two allele copies are identical in an individual they are said to be homozygous

When the two allele copies are different in an individual they are said to be heterozygous

The genotype of an individual affects their phenotype

A phenotype is the observable characteristics of an organism

Example of genotype & phenotype

Every horse has two copies of the coat colour gene in all of their cells

A horse that has two black coat alleles A has the genotype AA and is homozygous. The
phenotype of this horse would be a black coat

In contrast a horse that has one black coat allele A and one chestnut coat allele a would have
the genotype Aa and is heterozygous

Dominance
Not all alleles affect the phenotype in the same way

Some alleles are dominant: they are always expressed in the phenotype
This means they are expressed in both heterozygous and homozygous individuals

Other are recessive: they are only expressed in the phenotype if no dominant allele is
present
This means that it is only expressed when present in a homozygous individual

Example of dominance
If for horses the allele A for a black coat is dominant and the allele a for a chestnut coat is
recessive the following genotypes and phenotypes occur:
Genotype AA → black coat

Genotype Aa → black coat

Genotype aa → chestnut coat

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Codominance
Sometimes both alleles can be expressed in the phenotype at the same time

This is known as codominance

When an individual is heterozygous they will express both alleles in their phenotype

When writing the genotype for codominance the gene is symbolised as the capital letter and

the alleles are represented by different superscript letters, for example IA

Example of codominance
A good example of codominance can be seen in human blood types

The gene for blood types is represented in the genotype by I and the three alleles for human
blood types are represented by A, B and O

Allele A results in blood type A (IAIA or IAIO) and allele B results in blood type B (IBIB or IBIO)

If both allele A and allele B are present in a heterozygous individual they will have blood type

AB (IAIB)

Blood type O (IOIO) is recessive to both group A and group B alleles

F1, F2 & test crosses

When a homozygous dominant individual is crossed with a homozygous recessive
individual the offspring are called the F1 generation
All of the F1 generation are heterozygous

If two individuals from the F1 generation are then crossed, the offspring they produce are
called the F2 generation

A test cross can be used to try and deduce the genotype of an unknown individual
that is expressing a dominant phenotype
The individual in question is crossed with an individual that is expressing the
recessive phenotype

The resulting phenotypes of the offspring provide sufficient information to suggest the
genotype of the unknown individual

If there are any offspring expressing the recessive phenotype then the unknown
individual must have a heterozygous genotype

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Linkage
There are two types of linkage in genetics: sex linkage and autosomal linkage

Sex linkage:
There are two sex chromosomes: X and Y

Women have two copies of the X chromosome (XX) whereas men have one X
chromosome and one shorter Y chromosome (XY)

Some genes are found on a region of a sex chromosome that is not present
on the other sex chromosome

As the inheritance of these genes is dependent on the sex of the individual they
are called sex-linked genes

Most often sex-linked genes are found on the longer X chromsome

Haemophilia is well known example of a sex-linked disease

Sex-linked genes are represented in the genotype by writing the alleles as superscript
next to the sex chromosome. For example a particular gene that is found only on the
X chromosome has two alleles G and g. The genotype of a heterozygous female

would be written as XGXg. A males genotype would be written as XGY

Autosomal linkage:
This occurs on the autosomes (any chromosome that isn’t a sex chromosome)

Two or more genes on the same chromosome do not assort independently during
meiosis

These genes are linked and they stay together in the original parental combination

Exam Tip

When referring to the different alleles be careful about your notation. When
describing a dominant allele use capitals (for example allele B ) and when
describing a recessive allele use lower case ( for example allele b ). Be careful
when choosing the letters to represent the alleles when writing the genotype.
Use letters that are easy to distinguish between the capital and the lower
case (eg. B and b).

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16.2.2 PREDICTING INHERITANCE: MONOHYBRID CROSSES

Predicting Inheritance: Monohybrid Crosses

Monohybrid inheritance looks at how the alleles for a single gene are passed on from
one generation to the next

Known information about the genotypes, phenotypes and the process of meiosis are used to
make predictions about the phenotypes of offspring that would result from specific breeding
pairs

When two individuals sexually reproduce there is an equal chance of either allele from their
homologous pair making it into their gametes and subsequently the nucleus of the zygote
This means there is an equal chance of the zygote inheriting either allele from
their parent

Genetic diagrams are often used to present this information in a clear and precise manner so
that predictions can be made
These diagrams include a characteristic table called a Punnett square

The predicted genotypes that genetic diagrams produce are all based on chance
There is no way to predict which gametes will fuse so sometimes the observed or real-
life results can differ from the predictions

Worked example: Genetic diagram

One of the genes for the coat colour of horses has the following two alleles:
B, a dominant allele produces a black coat when present

b, a recessive allele produces a chestnut coat when present in a homozygous

individual

In this example a heterozygous male is crossed with heterozygous female

Parental phenotype: black coat x black coat

Parental genotype: Bb Bb

Parental gametes: B or b B or b

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Monohybrid punnett square with heterozygotes table

Predicted ratio of phenotypes in offspring – 3 black coat : 1 chestnut coat

Predicted ratio of genotypes in offspring – 1 BB : 2 Bb : 1 bb

Codominance
When working with codominant alleles the genetic diagrams can be constructed in a similar
way, however the genotypes are represented using a capital letter for the gene and

superscript letters for the alleles (eg. IAIA)

There will be more possible phenotypes and so the predicted ratios will be different

Worked example: Codominance

The gene for blood type has three alleles:
A, a dominant allele produces blood type A

B, a dominant allele produces blood type B

O, two recessive alleles will produce blood type O

In this example a blood type A person is crossed with a blood type B person

Parental phenotype: Blood type A x Blood type B

Parental genotype: IAIO IBIO

Parental gametes: IA or IO IB or IO

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Monohybrid punnett square with codominance table

Predicted ratio of phenotypes in offspring – 1 Blood type AB : 1 Blood type A : 1 Blood type B : 1
Blood type O

Predicted ratio of genotypes in offspring: 1 IAIB : 1 IAIO : 1 IBIO : IOIO

Sex-linkage
Sex-linked genes are only present on one sex chromosome and not the other

This means the sex of an individual affects what alleles they pass on to their offspring
through their gametes

If the gene is on the X chromosome males (XY) will only have one copy of the gene,
whereas females (XX) will have two

There are three phenotypes for females – normal, carrier and has the disease, whereas
males have only two phenotypes – normal or has the disease

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Worked example: Sex-linkage

Haemophilia is a well known sex-linked disease

There is a gene found on the X chromosome that codes for a protein called factor VIII.
Factor VIII is needed to make blood clot

There are two alleles for factor VIII, the dominant F allele which codes for normal factor VIII
and the recessive f allele which results in a lack of factor VIII

When a person possesses only the recessive allele f, they don’t produce factor VIII and their
blood can’t clot normally

The genetic diagram below shows how two parents with normal factor VIII can have offspring
with haemophilia

Parental phenotypes: carrier female x normal male

Parental genotypes: XFXf XFY

Parental gametes: XF or Xf XF or Y

Monohybrid punnett square with sex-linkage table

Predicted ratio of phenotypes in offspring – 1 female with normal blood clotting : 1 carrier female : 1
male with haemophilia : 1 male with normal blood clotting

Predicted ratio of genotypes in offspring: 1 XFXF : 1 XFXf : 1 XFY : 1 XfY

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Exam Tip

Make sure to include all of your working out when constructing genetic
diagrams. It is not enough just to complete a punnett square, you need to
show that you have thought about the possible gametes that can be
produced by each parent.
Also, remember to state the phenotype as well as the genotype of the
offspring that result from the cross. Read the questions carefully when
answering sex-linked inheritance questions – is the question asking for a
probability for all children or is it asking about a specific gender (boys or
girls).

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16.2.3 PREDICTING INHERITANCE: DIHYBRID CROSSES

Predicting Inheritance: Dihybrid Crosses

Monohybrid crosses look at how the alleles of one gene transfer across generations

Dihybrid crosses look at how the alleles of two genes transfer across generations

The genetic diagrams for both types of crosses are very similar

There are several more genotypes and phenotypes involved

When writing the different genotypes write the two alleles for one gene, followed
immediately by the two alleles for the other gene. Do not mix up the alleles from the
different genes
If there was a gene with alleles Y and y and another gene with alleles G and g an
example genotype for an individual would be YYGg

Worked example: Dihybrid genetic diagram

Horses have a single gene for coat colour that has two alleles:
B, a dominant allele produces a black coat

b, a recessive allele produces a chestnut coat

Horses also have single gene for eye colour

E, a dominant allele produces brown eyes

e, a recessive allele produces blue eyes

In this example a horse which is heterozygous for both genes has been crossed with a
horse that is homozygous for one gene and heterozygous for the other

Parental phenotypes: black coat, brown eyes x chestnut coat, brown eyes

Parental genotypes: BbEe bbEe

Parental gametes: BE or Be or bE or be bE or be

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Dihybrid cross punnett square table

Predicted ratio of phenotypes in offspring – 3 black coat, brown eyes : 3 chestnut coat, brown eyes :
1 black coat, blue eyes : 1 chestnut coat, blue eyes

Autosomal linkage
Dihybrid crosses and their predictions rely on the assumption that the genes being
investigated behave independently of one another during meiosis

Not all genes assort independently during meiosis

Some genes which are located on the same chromosome display autosomal linkage and
stay together in the original parental combination

Linkage between genes affects how parental alleles are passed onto offspring through the
gametes

When writing linked genotypes it can be easier to keep the linked alleles within a bracket
For example an individual has the genotype FFGG however if there is linkage
between the two genes then it would be written as (FG)(FG)

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Worked example: Explaining autosomal linkage

The genes for tail length and scale colour in a species of newt have displayed autosomal
linkage

The gene for tail length has two alleles :

Dominant allele T produces a normal length tail

Recessive allele t produces a shorter length tail

The gene for scale colour has two alleles:

Dominant allele G produces green scales

Recessive allele g produces white scales

A newt heterozygous for a normal tail and green scales is crossed with a newt that has a
shorter tail and white scales

Parental phenotypes: normal tail, green scales x short tail, white scales

Parental genotypes: (TG)(tg) (tg)(tg)

Parental gametes: (TG) or (tg) (tg)

Dihybrid cross with linkage punnett square table

Predicted ratio of phenotypes in offspring – 1 normal tail, green scales : 1 short tail, white scales

Predicted ratio of genotypes in offspring – 1 (TG)(tg) : 1 (tg)(tg)

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16. Inheritance ⬇

Epistasis
In some cases one gene can affect the expression of another gene

Epistasis: when two genes on different chromosomes affect the same feature

If epistasis is present it needs to be taken into account when determining the phenotypes of
individuals

The whole combination of alleles from the different genes dictates the phenotype

Worked example: Explaining epistasis

There is a gene that dictates the feather colour of pigeons

The gene has two alleles (R / r) :

Allele R codes for a pigment that produces grey feathers

Allele r doesn’t produce a pigment, resulting in white feathers

Another gene has also been found to have an effect on feather colour

This gene has two alleles (F / f) :

The dominant allele F stops grey feathers being produced even if the allele R is
present

These are the possible phenotypes:

RRFF white feathers

RrFF white feathers

rrFF white feathers

RRFf white feathers

RrFf white feathers

rrFf white feathers

rrff white feathers

RRff grey feathers

Rrff grey feathers

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Exam Tip

When you are working through different genetics questions you may notice
that test crosses involving autosomal linkage predict solely parental type
offspring (offspring that have the same combination of characteristics as their
parents).
However in reality recombinant offspring (offspring that have a different
combination of characteristics to their parents) are often produced. This is
due to the crossing over that occurs during meiosis. The crossing over and
exchanging of genetic material breaks the linkage between the genes and
recombines the characteristics of the parents.
So if a question comes along that asks you why recombinant offspring are
present you now know why!

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16. Inheritance ⬇

16.2.4 PREDICTING INHERITANCE: TEST CROSSES

Predicting Inheritance: Test Crosses

A test cross can be used to deduce the genotype of an unknown individual that is
expressing a dominant phenotype

The individual in question is crossed with an individual that is expressing the recessive
phenotype

This is because an individual with a recessive phenotype has a known genotype

The resulting phenotypes of the offspring provides sufficient information to suggest the
genotype of the unknown individual

Results
For a monohybrid test cross:
If no offspring exhibit the recessive phenotype then the unknown genotype is
homozygous dominant

If at least one of the offspring exhibit the recessive phenotype then the unknown
genotype is heterozygous

For a dihybrid test cross:

If no offspring exhibit the recessive phenotype for either gene then the unknown
genotype is homozygous dominant for both genes

If at least one of the offspring exhibit the recessive phenotype for one gene but not
the other, then the unknown genotype is heterozygous for one gene and
homozygous dominant for the other

If at least one of the offspring exhibit the recessive phenotype for both genes then the
unknown genotype is heterozygous for both genes

Worked example: Test crosses

Rabbits have a single gene for ear length that has two alleles:
D, a dominant allele that produces long ears

d, a recessive allele that produces shorter ears

A breeder has a rabbit called Floppy that has long ears and they want to know the genotype
of the rabbit
There are two possibilities: DD or Dd

The breeder crosses the long-eared rabbit with a short-eared rabbit

A rabbit displaying the recessive short ear phenotype has to have the genotype dd

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16. Inheritance ⬇

Test cross possibility one table

Predicted ratio of phenotypes of offspring – 1 long ears

Predicted ratio of genotypes of offspring – 1 Dd

Test cross possibility two table

Predicted ratio of phenotypes of offspring – 1 long ears : 1 short ears

Predicted ratio of genotypes of offspring – 1 Dd : 1 dd

The breeder identifies the different phenotypes present in the offspring

There is at least one offspring with the short ear phenotype

This tells the breeder that their rabbit Floppy has the genotype Dd

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If Floppy was genotype DD none of the offspring would have short ears

Exam Tip

Make sure before you start a test cross you think about the following: how
many genes are there, how many alleles of each gene are there, which is the
dominant allele, what type of dominance is it and is there linkage or epistasis
between genes?

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16. Inheritance ⬇

16.2.5 PREDICTING INHERITANCE: CHI-SQUARED TEST

Predicting Inheritance: Chi-squared Test

The difference between expected and observed results in experiments can be

statistically significant or insignificant (happened by chance)

If the difference between results is statistically significant it can suggest that something
else is happening in the experiment that isn’t being accounted for
For example linkage between genes

A statistical test called the chi-squared test determines whether there is a significant
difference between the observed and expected results in an experiment

The chi-squared test is completed when the data is categorical (data that can be grouped)

Calculating chi-squared values

Obtain the expected and observed results for the experiment

Calculate the difference between each set of results

Square each difference (as it is irrelevant whether the difference is positive or negative)

Divide each squared difference by the expected value and get a sum of these answers to
obtain the chi-squared value

Analysing chi-squared values

To work out what the chi-squared value means, a table that relates chi-squared values to
probabilities is used

If the chi-squared value represents a larger probability than the critical probability
then it can be stated that the differences between the expected and observed results are
due to chance

If it represents a smaller probability than the critical probability then the differences in
results are significant and something else may be causing the differences

To determine the critical probability biologists generally use a probability of 05 (they allow
that chance will cause five out of every 100 experiments to be different)

The number of comparisons made must also be taken into account when determining the
critical probability. This is known as the degrees of freedom

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16. Inheritance ⬇

Worked example: Chi-squared test

An experiment was carried out investigating the inheritance of two genes in rabbits; one for coat
colour and one for ear length. A dihybrid cross revealed the expected ratio of phenotypes to be 9 : 3
: 3 : 1. Several rabbits with the heterozygous genotype were bred together and the phenotypes of all
the offspring were recorded. The ratio of the offspring was not exactly what was predicted. In order
to determine whether this was due to chance or for some other reason, the chi-squared test was
used.

Chi-squared worked example table

The expected ratio is calculated by multiplying the total number of organisms ( 128 rabbits) with
each expected ratio:

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16. Inheritance ⬇

In order to understand what this chi-squared value of 0.56 says about the data, a table
relating chi-squared values to probability is needed

The chi-squared table displays the probabilities that the differences between expected and
observed are due to chance

The degrees of freedom can be worked out from the results. It is calculated by
subtracting one from the number of classes
In this example there are four phenotypes which means four classes, 4 – 1 = 3

This means that the values in the third row are important for comparison

For this experiment there is a critical probability of 0.05

This means that 7.82 is the value used for comparison

The chi-squared value from the results (0.56) is much smaller than 7.82

56 would be located somewhere to the left-hand side of the table, representing a probability
much greater than 0.1

This means that there is no significant difference between the expected and observed
results, any differences that do occur are due to chance

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16. Inheritance ⬇

Exam Tip

When calculating a chi-squared value it is very helpful to create a table like

the one seen in the worked example. This will help you with your calculations
and make sure you don’t get muddled up!
You should also be prepared to suggest reasons why results might be
significantly different. For example, there could be linkage between the
genes being analysed.

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16. Inheritance ⬇

16.2.6 GENES, PROTEINS & PHENOTYPE

Genes, Proteins & Phenotype

A gene can affect a phenotype of an organism

A gene codes for a single protein

The protein affects the phenotype through a particular mechanism

The phenotype of an individual can also be affected by the environment

TYR gene & albinism

Humans with albinism lack the pigment melanin in their skin, hair and eyes
This causes them to have very pale skin, very pale hair and pale blue or pink irises in the
eyes

There is a metabolic pathway for producing melanin:

1. The amino acid tyrosine is converted to DOPA by the enzyme tyrosinase

2. DOPA is converted to dopaquinone again by the enzyme tyrosinase

3. Dopaquinone is converted to melanin

tyrosine → DOPA → dopaquinone → melanin

A gene called TYR located on chromosome 11 codes for the enzyme tyrosinase

There is a recessive allele for the gene TYR that causes a lack of enzyme tyrosinase or the
presence of inactive tyrosinase
Without the tyrosinase enzyme tyrosine can not be converted into melanin

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16. Inheritance ⬇

HBB gene & sickle cell anaemia

Sickle cell anaemia is a condition that causes individuals to have frequent infections,
episodes of pain and anaemia

Humans with sickle cell anaemia have abnormal haemoglobin in their red blood cells

β-globin is a polypeptide found in haemoglobin that is coded for by the gene HBB which is
found on chromosome 11

There is an abnormal allele for the gene HBB which produces a slightly different amino acid
sequence to the normal allele
The change of a single base in the DNA of the abnormal allele results in an amino acid
substitution (the base sequence CTT is replaced by CAT)

This change in amino acid sequence (the amino acid Glu is replaced with Val)
results in an abnormal β-globin polypeptide

The abnormal β-globin in haemoglobin affects the structure and shape of the red blood
cells
They are pulled into a half moon shape

They are unable to transport oxygen around the body

They stick to each other and clump together blocking capillaries

A homozygous individual that has two abnormal alleles for the HBB gene produces only sickle
cell haemoglobin
They have sickle cell anaemia and suffer from the associated symptoms

A heterozygous individual that has one normal allele and one abnormal allele for the HBB
gene will produce some normal haemoglobin and some sickle cell haemoglobin
They are a carrier of the allele

They may have no symptoms

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F8 gene & haemophilia

Factor VIII is a coagulating agent that plays an essential role in blood clotting

The gene F8 codes for the Factor VIII protein

There are abnormal alleles of the F8 gene that result in:

Production of abnormal forms of factor VIII

Less production of normal factor VIII

No production of factor VIII

A lack of normal factor VIII prevents normal blood clotting and causes the condition
haemophilia

The F8 gene is located on the X chromosome

This means F8 is a sex-linked gene

Haemophilia is a sex-linked condition

If males have an abnormal allele they will have the condition as they have only one
copy of the gene

Females can be heterozygous for the F8 gene and not suffer from the condition but
act as a carrier

HTT gene & Huntington’s disease

Huntington’s disease is a genetic condition that develops as a person ages

Usually a person with the disease will not show symptoms until they are 30 years old +

An individual with the condition experiences neurological degeneration; they lose their
ability to walk, talk and think

The disease is ultimately fatal

It has been found that individuals with Huntington’s disease have abnormal alleles of the
HTT gene
The HTT gene codes for the protein huntingtin which is involved in neuronal
development

People that have a large number (>40) of repeated CAG triplets present in the
nucleotide sequence of their HTT gene suffer from the disease

The abnormal allele is dominant over the normal allele

If an individual has one abnormal allele present they will suffer from the disease

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16. Inheritance ⬇

Gene, protein & phenotype summary table

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16. Inheritance ⬇

Exam Tip

You may be asked to predict the inheritance of diseases like the ones above.
An example question would be:
Max and Jane are trying for a baby but they are concerned about the
possibility of their child having haemophilia. Neither Max or Jane have
haemophilia themselves but Jane’s father had the condition. What are
chances that their child could have haemophilia?
For questions like this, it is very important to gather early on whether the
abnormal allele that causes the disease is dominant or recessive and if there
is any sex linkage. In this example for haemophilia, the abnormal allele is
recessive and the gene is sex-linked.
Then the next step would be to work out the genotypes of the parents from
the information given and use this to create a genetic diagram.

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16. Inheritance ⬇

16.2.7 THE ROLE OF GIBBERELLIN IN STEM ELONGATION

The Role of Gibberellin in Stem Elongation

In some plants species their height is partially controlled by their genes

The Le gene dictates the height of some plants

It has two alleles: Le and le

The dominant allele Le produces tall plants when present

The recessive allele le produces shorter plants when present (in a homozygous
individual)

The gene regulates the production of an enzyme that is involved in a pathway that forms
active gibberellin GA1

Active gibberellin is a hormone that helps plants grow by stimulating cell division and
elongation in the stem

The recessive allele le results in non-functional enzyme

It is only one nucleotide different to the dominant allele

This causes a single amino acid substitution (threonine -> alanine) in the primary
structure of the enzyme

This change in primary structure occurs at the active site of the enzyme, making it
non-functional

Without this enzyme no active gibberellin is formed and plants are unable to grow tall

Plants that are homozygous for the recessive allele le are dwarves

Some farmers apply active gibberellin to shorter plants to stimulate growth

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16. Inheritance ⬇

16.3 GENE CONTROL

16.3.1 GENE CONTROL

Gene Control

The nucleus of every cell in the human body contains the same genes
However not every gene is expressed in every cell

Not all of these genes are expressed all the time

There are several mechanisms that exist within cells to make sure the correct genes are
expressed in the correct cell at the right time
They involve regulatory genes

Structural & regulatory genes

A structural gene codes for a protein that has a function within a cell
For example, the F8 gene codes for the protein Factor VIII involved in blood clotting

A regulatory gene codes for a protein that helps to control the expression of another gene

Structural and regulatory genes that work together are usually found close together

Inducible & repressible enzymes

Some genes code for proteins that form enzymes

Some enzymes are required all the time and some are required only at specific times

The expression of enzyme-producing genes can be controlled

Inducible enzymes are only synthesized when their substrate is present

The presence of the substrate induces the synthesis of of the enzyme by causing
the transcription of the gene for the enzyme to start

Repressible enzymes are synthesized as normal until a repressor protein binds to an

operator
The presence of the repressor protein represses the synthesis of the enzyme by
causing the transcription of the gene for the enzyme to stop

Controlling when enzymes are synthesized can be beneficial for cells as it stops materials
and energy being wasted
For example, using materials and energy to synthesize an enzyme when its substrate
is not present and it can’t carry out its function would be highly wasteful

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16. Inheritance ⬇

16.3.2 GENE CONTROL: LAC OPERON

Gene Control: Lac Operon

Regulatory genes control structural genes and their levels of protein production

Regulatory genes sometimes have control over several structural genes at once

Structural genes in prokaryotes can form an operon: a group or a cluster of genes that are
controlled by the same promoter

The lac operon found in some bacteria is one of the most well-known of these

The lac operon controls the production of the enzyme lactase (also called β-galactosidase)
and two other structural proteins

Lactase breaks down the substrate lactose so that it can be used as an energy source in the
bacterial cell

It is an inducible enzyme that is only synthesized when lactose is present

This helps prevent the bacteria from wasting energy and materials

Structure of the lac operon

The components of the lac operon are found in the following order:
Promoter for structural genes

Operator

Structural gene lacZ that codes for lactase

Structural gene lacY that codes for permease (allows lactose into the cell)

Structural gene lacA that codes for transacetylase

Located to the left (upstream) of the lac operon on the bacterium’s DNA there is also the:
Promoter for regulatory gene

Regulatory gene lacI that codes for the lac repressor protein

The lac repressor protein has two binding sites that allow it to bind to the operator in the
lac operon and also to lactose (the effector molecule)
When it binds to the operator it prevents the transcription of the structural genes
as RNA polymerase cannot attach to the promoter

When it binds to lactase the shape of the repressor protein distorts and it can no
longer bind to the operator

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16. Inheritance ⬇

When lactose is absent

The following processes take place when lactose is absent in the medium that the bacterium
is growing in:
The regulatory gene is transcribed and translated to produce lac repressor protein

The lac repressor protein binds to the operator region upstream of lacZ

Due to the presence of the repressor protein RNA polymerase is unable to bind to
the promoter region

Transcription of the structural genes does not take place

No lactase enzyme is synthesized

When lactose is present

The following processes take place when lactose is present in the medium that the bacterium
is growing in:
There is an uptake of lactose by the bacterium

The lactose binds to the second binding site on the repressor protein,
distorting its shape so that it cannot bind to the operator site

RNA polymerase is then able to bind to the promoter region and transcription
takes place

The mRNA from all three structural genes is translated

Enzyme lactase is produced and lactose can be broken down and used for energy
by the bacterium

Exam Tip

The example above explains how the genetic control of an inducible enzyme
works. You could get some questions on the genetic control of repressible
enzymes.
In this mechanism an effector molecule also binds to a repressor protein
produced by a regulatory gene. However this binding actually helps the
repressor bind to the operator region and prevent transcription of the
structural genes. So it’s the opposite of the lac operon: when there is less of
the effector molecule, the repressor protein cannot bind to the operator
region and transcription of the structural genes goes ahead, meaning
the enzyme is produced.

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16. Inheritance ⬇

16.3.3 GENE CONTROL: TRANSCRIPTION FACTORS

Gene Control: Transcription Factors

Prokaryotes use operons to control the expression of genes in cells

Eukaryotes also use transcription factors to control gene expression

A transcription factor is a protein that controls the transcription of genes by binding to a

specific region of DNA

They ensure that genes are being expressed in the correct cells, at the correct time and to
the right level

It is estimated that ~10% of human genes code for transcription factors

There are several types of transcription factors that have varying effects on gene
expression

This is still a relatively young area of research and scientists are working hard to
understand how all the different transcription factors function

Transcription factors allow organisms to respond to their environment

Some hormones achieve their effect via transcription factors

How transcription factors work

Some transcription factors bind to the promoter region of a gene
This binding can either allow or prevent the transcription of the gene from taking
place

The presence of a transcription factor will either increase or decrease the rate of
transcription of a gene

For example, PIF is a transcription factor found in plants that activates the transcription of
the amylase gene

Gene Control: Gibberellin

Plant cells use transcription factors in a similar way to animal cells

Gibberellin is a hormone found in plants (e.g. wheat and barley) that controls seed
germination by stimulating the synthesis of the enzyme amylase

It does this by influencing transcription of the amylase gene

When gibberellin is applied to a germinating seed there is an increased amount of the
mRNA for amylase present

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Mechanism
The breakdown of DELLA protein by gibberellin is necessary for the synthesis of
amylase

The following components are involved:

Repressor protein DELLA

Transcription factor PIF

Promoter of amylase gene

Amylase gene

Gibberellin

Gibberellin receptor and enzyme

The process occurs as follows:

DELLA protein is bound to PIF, preventing it from binding to the promoter of the
amylase gene so no transcription can occur

Gibberellin binds to a gibberellin receptor and enzyme which starts the breakdown of
DELLA

PIF is no longer bound to DELLA protein and so it binds to the promoter of the amylase
gene

Transcription of amylase gene begins

Amylase is produced

Exam Tip

In your exam you may be asked to explain why RNA analysis is important with
regards to gene expression. From the outside most cells look almost identical
with the same DNA in their nucleus. However we know that they are most
likely expressing different genes.
When a cell expresses a gene, RNA is produced by transcription. This RNA
present in a cell can be analysed. Scientists can match the RNA present in a
cell to specific genes and work out which genes are being expressed in that
specific cell.

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17. Selection & Evolution ⬇

CONTENTS
17.1 Variation
17.1.1 Variation: Phenotype

17.1.2 Variation: Discontinuous & Continuous

17.1.3 Variation: t-test Method

17.1.4 Variation: t-test Worked Example

17.2 Natural & Artificial Selection

17.2.1 Natural Selection

17.2.2 Natural Selection: Types of Selection

17.2.3 Natural Selection: Changes in Allele Frequencies

17.2.4 Natural Selection: Antibiotic Resistance

17.2.5 Natural Selection: Hardy-Weinberg Principle

17.2.6 Artificial Selection

17.2.7 Examples of Artificial Selection

17.3 Evolution
17.3.1 Theory of Evolution

17.3.2 Allopatric & Sympatric Speciation

17.1 VARIATION

17.1.1 VARIATION: PHENOTYPE

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17. Selection & Evolution ⬇

Variation: Phenotype

The observable characteristics of an organism are its phenotype

Phenotypic variation is the difference in phenotypes between organisms of the same

species

In some cases, phenotypic variation is explained by genetic factors

For example, the four different blood groups observed in human populations are due
to different individuals within the population having two of three possible alleles for
the single ABO gene

In other cases, phenotypic variation is explained by environmental factors

For example, clones of plants with exactly the same genetic information (DNA) will
grow to different heights when grown in different environmental conditions

Phenotypic variation can also be explained by a combination of genetic and

environmental factors
For example, the recessive allele that causes sickle cell anaemia has a high frequency
in populations where malaria is prevalent due to heterozygous individuals being
resistant to malaria

The complete phenotype of an organism is determined by the expression of its genotype and
the interaction of the environment on this:

Phenotype = Genotype + Environment

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17. Selection & Evolution ⬇

Genetic variation
Organisms of the same species will have very similar genotypes, but two individuals
(even twins) will have differences between their DNA base sequences

Considering the size of genomes, these differences are small between individuals of
the same species

The small differences in DNA base sequences between individual organisms within a
species population is called genetic variation

Genetic variation is transferred from one generation to the next and it generates
phenotypic variation within a species population

Genetic variation is caused by the following processes as they result in a new

combination of alleles in a gamete or individual:
Independent assortment of homologous chromosomes during metaphase I

Crossing over of non-sister chromatids during prophase I

Random fusion of gametes during fertilization

Mutation results in the generation of new alleles

The new allele may be advantageous, disadvantageous or have no apparent
effect on phenotype (due to the fact that the genetic code is degenerate

New alleles are not always seen in the individual that they first occur in

They can remain hidden (not expressed) within a population for several
generations before they contribute to phenotypic variation

Genes can have varying effects on an organism’s phenotype

The phenotype may be affected by a single gene or by several

The effect that the gene has on the phenotype may be large, small and/or
additive

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17. Selection & Evolution ⬇

Sources of genetic variation table

Environmental factors
The environment that an organism lives in can also have an impact on its phenotype

Different environments around the globe experience very different conditions in terms of the:
Length of sunlight hours (which may be seasonal)

Supply of nutrients (food)

Availability of water

Temperature range

Oxygen levels

Changes in the factors above can affect how organisms grow and develop
For example, plants with a tall genotype growing in an environment that is depleted in
minerals, sunlight and water will not be able to grow to their full potential size
determined by genetics

Variation in phenotype caused solely by environmental pressures or factors cannot be

inherited by an organism’s offspring
Only alterations to the genetic component of gametes will ever be inherited

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17. Selection & Evolution ⬇

Exam Tip

Some questions in the exam may ask you to explain why the variation in
phenotype due to genetics is inherited but the variation in phenotype due to
environmental factors is not. This is because genetic variation directly affects
the DNA of the gametes but variation in phenotype caused by the
environment does not.

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17. Selection & Evolution ⬇

17.1.2 VARIATION: DISCONTINUOUS & CONTINUOUS

Variation: Discontinuous & Continuous

The term variation refers to the differences that exist between at least two things (be it a
level, amount, quantity or feature of something)

In relation to natural selection, variation refers to the differences that exist between
individuals of a species
This may also be referred to as intraspecific variation

Variation observed in the phenotypes of organisms can be due to qualitative or quantitative

differences

Discontinuous variation
Qualitative differences in the phenotypes of individuals within a population give rise to
discontinuous variation

Qualitative differences fall into discrete and distinguishable categories, usually with no
intermediates (a feature can’t fall in between categories)
For example, there are four possible ABO blood groups in humans; a person can only
have one of them

It is easy to identify discontinuous variation when it is present in a table or graph due to the
distinct categories that exist when data is plotted for particular characteristics

Graph showing population variation in blood types: an example of discontinuous

variation with qualitative differences

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Continuous variation
Continuous variation occurs when there are quantitative differences in the phenotypes of
individuals within a population for particular characteristics

Quantitative differences do not fall into discrete categories like in discontinuous variation

Instead for these features, a range of values exist between two extremes within which the
phenotype will fall
For example, the mass or height of a human is an example of continuous variation

The lack of categories and the presence of a range of values can be used to identify
continuous variation when it is presented in a table or graph

Graph showing population variation in height: an example of continuous variation with

quantitative differences

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17. Selection & Evolution ⬇

The Genetic Basis of Variation

Discontinuous variation refers to the differences between individuals of a species where

the differences are qualitative (categoric)

Continuous variation is the differences between individuals of a species where the

differences are quantitative (measurable)

Each type of variation can be explained by genetic and / or environmental factors

Genetic basis of discontinuous variation

This type of variation occurs solely due to genetic factors

The environment has no direct effect

Phenotype = genotype

At the genetic level:

Different genes have different effects on the phenotype

Different alleles at a single gene locus have a large effect on the phenotype

Remember diploid organisms will inherit two alleles of each gene, these alleles can be
the same or different

A good example of this is the F8 gene that codes for the blood-clotting protein Factor VIII
The different alleles at the F8 gene locus dictate whether or not normal Factor VIII is
produced and whether the individual has the condition haemophilia

Genetic basis of continuous variation

This type of variation is caused by an interaction between genetics and the
environment

Phenotype = genotype + environment

At the genetic level:

Different alleles at a single locus have a small effect on the phenotype

Different genes can have the same effect on the phenotype and these add together
to have an additive effect

If a large number of genes have a combined effect on the phenotype they are known
as polygenes

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17. Selection & Evolution ⬇

The additive effect of genes

The height of a plant is controlled by two unlinked genes H / h and T / t

The two genes have an additive effect

The recessive alleles h and t contribute x cm to the plants height

The dominant alleles H and T contribute 2x cm to the plants height

The following genotypes will have the following phenotypes:

h h t t : x + x + x + x = 4x cm

H H T T : 2x + 2x + 2x + 2x = 8x cm

H h T t : 2x + x + 2x + x = 6x cm

H H T t : 2x + 2x + 2x + x = 7x cm

H h T T : 2x + x + 2x + 2x = 7x cm

h h T t : x + x + 2x + x = 5x cm

H h t t : 2x + x + x + x = 5x cm

Exam Tip

Be careful when answering questions that involve polygenes or genes with an

additive effect. It is not a given that each gene will have the same effect on
the phenotype as in the example above so make sure to double check the
information you have been given in the question.

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17. Selection & Evolution ⬇

17.1.3 VARIATION: T-TEST METHOD

Variation: t-test Method

A statistical test called the t-test can be used to compare the means of two sets of data
and determine whether they are significantly different or not
The formula for the t-test will be provided in the exam, but formulate for how to
calculate the number of degrees of freedom is not provided in the exam and must
be learnt

The sets of data must follow a rough normal distribution, be continuous and the
standard deviations should be approximately equal

The standard deviation (s) must be calculated for each data set before the t-test can be
carried out

A null hypothesis should also be given

This is a statement of what we would expect if there is no significant difference between

two means, and that any differences seen are due to change

If there is a statistically significant difference between the means of two sets of data, then
the observation is not down to chance and the null hypothesis can be rejected

Calculating the standard deviation

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17. Selection & Evolution ⬇

Using the t-test to compare two means

The steps below outline the general steps in a t test; for a worked example see the next page

Null hypothesis: there is no statistically significant difference between the means of sample 1
and sample 2

Step 1: Calculate the mean for each data set:

Step 2: Calculate the standard deviation for each set of data, s1 = standard deviation of
sample 1 and s2 = standard deviation of sample 2

Step 3: Square the standard deviation and divide by n (the number of observations) in each
sample, for both samples:

Step 4: Add the values from step 3 together and take the square root:

Step 5: Divide the difference between the two means (see step 1) with the value calculated
in step 4 to get the t value:

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Step 6: Calculate the degrees of freedom (v) for the whole data set (remember the
formulae for this will not be given in the exam):

v = (n1 – 1) + (n2 – 1)

Step 7: Look at a table that relates t values to the probability that the differences between
data sets is due to chance to find where the t value for the degrees of freedom (v) calculated
lies

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17. Selection & Evolution ⬇

T values table

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Step 8: The greater the t value calculated (for any degree of freedom), the lower the
probability of chance causing any significant difference between the two sample means
Identify where the t value calculated lies with respect to the confidence levels
provided

If the t value is greater than the critical value (obtained from the table at the
critical probability of 0.05) then any difference between the two data sets is less likely
to be due to chance, so the null hypothesis can be rejected

If the t value is less than the critical value given at a confidence of 5%/ the probability
that any difference is down to chance is above 0.05; then an assumption can be made
that the differences between the means of the two sets of data are not significant and
the null hypothesis is accepted

Using the table above, if a value of t was calculated to be 2.38 at 5 degrees of freedom, then
it lies between 2.02 and 2.57, so the probability that chance produced any differences
between the two means is between 10% and 5%; the null hypothesis would be accepted in
this situation

Exam Tip

If you need to calculate the t value you will be given the formula in the exam.
Generally questions on the t-test require you to:
• Know why a t-test is being used to analyse the data
• State the null hypothesis
• Know how the degrees of freedom was calculated
• State the conclusion (are the differences between the two means significant
or not)

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17. Selection & Evolution ⬇

17.1.4 VARIATION: T-TEST WORKED EXAMPLE

Variation: t-test Worked Example

Worked example: T-test

Solution

Null hypothesis: There is no significant difference between the ear lengths of the rabbits in
populations A and B

Sample sizes:
Population A: n1 = 15

Population B: n2 = 15

Step 1: Calculate the mean for each data set:

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Step 2: Calculate the standard deviation (s) for each set of data:

Worked example t-test table 1

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17. Selection & Evolution ⬇

Divide the sum of each square by n – 1 for each data set, and take the square root of each
value:

Worked example t-test table 2

Step 3 to 5: Sub all known values into the t-test equation by:
Step 3: Square the standard deviation and divide by n (the number of observations)
in each sample, for both samples:

Step 4: Add the values from step 3 together and find the square root

Step 5: Divide the difference between the two means by the value from step 4

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17. Selection & Evolution ⬇

Worked example t-test table 3

Step 6: Calculate the degrees of freedom (v) for all the data:
v = (n1 – 1) + (n2 – 1) = 14 + 14 = 28

Step 7: Look at a table that relates t values to the probability that the differences between
data sets is due to chance to find where the t value of 1.91 for 28 degrees of freedom (v)
calculated lies

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17. Selection & Evolution ⬇

T value worked example table

Step 8: Draw a conclusion about the statistical relevance of the data:

A t value of 1.91 represents a probability between 0.05 and 0.1 which is greater than
the critical value of 0.05.

This means the null hypothesis should be accepted, as there are no significant
differences between the two sets of results (any differences between the means of
the ear length of rabbits in the two populations are due to chance)

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17. Selection & Evolution ⬇

17.2 NATURAL & ARTIFICIAL SELECTION

17.2.1 NATURAL SELECTION

Natural Selection

Every individual within a species population has the potential to reproduce and have
offspring which contribute to population growth

If the offspring for every individual survived to adulthood and reproduced then the population
would experience exponential growth
This type of growth only happens when there are no environmental factors or
population checks acting on the population (for example, when there are plentiful
resources and no disease)

One well known but rare example of exponential growth in a population is the
introduction of 24 European rabbits into Australia in the 1800s. The rabbits had an
abundance of resources, little or no competition and no natural predators. This meant
the population increased rapidly and they became a major pest

In reality, there are several environmental factors that prevent every individual in a
population making it to adulthood and reproducing

Environmental factors
Environmental factors limit population sizes by reducing the rate of population growth
whenever a population reaches a certain size

Environmental factors can be biotic or abiotic

Biotic factors involve other living organisms

This includes things like predation, competition for resources and disease

Abiotic factors involve the nonliving parts of an environment

Examples of abiotic factors include light availability, water supply and soil pH

When biotic and abiotic factors come into play not all individuals within a population will
survive
For example, if a food source is limited some animals within a population will not get
enough to eat and will starve to death

For most populations in the wild, the number of offspring produced is much higher than the
number of individuals that make it adulthood

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17. Selection & Evolution ⬇

Population limitation by environmental factors

For African lions living in the wild there are several environmental factors that limit their
population growth rate:

1. Competition for food

There is a limited supply of prey: other lions and carnivores will also be hunting the
same prey. If a lion is not able to hunt and feed then they will die from starvation

2. Competition for a reproductive mate

Female lions will often outnumber male lions in a population. This means the males
compete with each other to mate with the females. When one male is in a contest
with another male one (or both) could be injured or killed. Whoever loses the contest
won’t be able to mate with the females in a pride and so won’t pass on his genes to
any offspring

3. Supply of water
African habitats can be very arid during the dry season. The water sources that the
lions drink from can be miles apart. If a lake or source of water dries up then they can
die due to dehydration

4. Temperature
The extreme heat experienced in the lion’s African habitat can cause them to
overheat and die. It can also prevent them from hunting for long periods during the
day, meaning they are less likely to get the food they need to survive

The combined effect of all these environmental factors leads to a decrease in population
growth as fewer individuals survive to adulthood and reproduce

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17. Selection & Evolution ⬇

Natural selection & survival

Variation exists within a species population

This means that some individuals within the population possess different phenotypes (due
to genetic variation in the alleles they possess; remember members of the same species will
have the same genes)

Environmental factors affect the chance of survival of an organism; they, therefore, act as a
selection pressure

Selection pressures increase the chance of individuals with a specific phenotype

surviving and reproducing over others

The individuals with the favoured phenotypes are described as having a higher fitness
The fitness of an organism is defined as its ability to survive and pass on its alleles
to offspring

Organisms with higher fitness posses adaptations that make them better suited to
their environment

When selection pressures act over several generations of a species they have an effect on
the frequency of alleles in a population through natural selection
Natural selection is the process by which individuals with a fitter phenotype are more
likely to survive and pass on their alleles to their offspring so that the advantageous
alleles increase in frequency over time and generations

Natural selection in rabbits

Variation in their fur colour exists within rabbit populations

At a single gene locus, normal brown fur is produced by a dominant allele whereas white
fur is produced by a recessive allele in a homozygous individual

Rabbits have natural predators like foxes which act as a selection pressure

Rabbits with a white coat do not camouflage as well as rabbits with brown fur, meaning
predators are more likely to see white rabbits when hunting

As a result, rabbits with white fur are less likely to survive than rabbits with brown fur

The rabbits with brown fur therefore have a selection advantage, so they are more likely
to survive to reproductive age and be able to pass on their alleles to their offspring

Over many generations, the frequency of alleles for brown fur will increase and the
frequency of alleles for white fur will decrease

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17. Selection & Evolution ⬇

Exam Tip

Remember that organisms better suited to their environments are more likely
to survive, but survival is not guaranteed. Organisms that are less suited to
an environment are still able to survive and potentially reproduce within it,
but their chance of survival and reproduction is lower than their better-suited
peers.
Also, it is important to be aware that an environment, and the selection
pressures it exerts on an organism, can change over time. When a change
occurs then a different phenotype may become fitter.
Finally, remember that all organisms (not just animals) experience selection
pressures as a result of the environment they are in!

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17. Selection & Evolution ⬇

17.2.2 NATURAL SELECTION: TYPES OF SELECTION

Natural Selection: Types of Selection

Environmental factors that affect the chance of survival of an organism are selection
pressures
For example, there could be high competition for food between lions if there is not
plentiful prey available; this environmental factor ‘selects’ for faster, more powerful
lions that are better hunters

These selection pressures can have different effects on the allele frequencies of a
population through natural selection

There are three types of selection:

Stabilising

Disruptive

Directional

Stabilising selection
Stabilising selection is natural selection that keeps allele frequencies relatively constant
over generations

This means things stay as they are unless there is a change in the environment

A classic example of stabilising selection can be seen in human birth weights

Very-low and very-high birth weights are selected against leading to the
maintenance of the intermediate birth weights

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17. Selection & Evolution ⬇

Directional selection
Directional selection is natural selection that produces a gradual change in allele
frequencies over several generations

This usually happens when there is a change in environment / selection pressures or a

new allele has appeared in the population that is advantageous

For example: A recent finding has shown that climate change is having an effect on fish size
in certain habitats
The increase in temperature is selecting for a smaller body size and against a
larger body size

Warmer seas cause fish metabolism to speed up and so increases their need for
oxygen; oxygen levels are lower in warmer seas

Larger fish have greater metabolic needs than smaller fish, and so they feel the
effect of increased temperatures more strongly

Organisms are sensitive to changes in temperature primarily because of the effect

that temperature can have on enzyme activity

Fish with a smaller body size are therefore fitter and better adapted to living in
seas experiencing increased temperatures

Fish body size is determined by both genetic and environmental factors

Fish of a smaller size are more likely to reproduce and pass on their alleles to
offspring

Over generations, this leads to an increase in the frequency of alleles that

produce a small body size and a decrease in the frequency of alleles that produce a
larger body size

Disruptive selection
Disruptive selection is natural selection that maintains high frequencies of two
different sets of alleles
In other words, individuals with intermediate phenotypes or alleles are selected
against

Disruptive selection causes polymorphism: the continued existence of two or more distinct
phenotypes in species

This can occur in an environment that shows variation

For example, birds that live on the Galapagos Islands use their beaks to forage for different
sized seeds
The size of the bird’s beaks are either small or large with the intermediate medium-
sized beak selected against

The reason for this is that the different types of seed available are more efficiently
foraged by a shorter or longer beak

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17. Selection & Evolution ⬇

Exam Tip

Become familiar with the shapes of the graphs above. They can help you
answer questions about the type of selection that is occurring in a population.

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17. Selection & Evolution ⬇

17.2.3 NATURAL SELECTION: CHANGES IN ALLELE FREQUENCIES

Natural Selection: Changes in Allele Frequencies

Natural selection causes a change in allele frequencies over time

Selection pressures (caused by the environment an organism is in) increase the
likelihood that certain individuals with specific alleles survive to reproductive age,
enabling them to pass on their alleles to their offspring

There are other factors or processes that can affect allele frequencies in a population:
The founder effect

Genetic drift

The bottleneck effect

Natural selection
When a new allele arises in a population or a change in the environment occurs then
directional selection can happen

Directional selection produces a gradual change in allele frequencies over several

generations
There is always phenotypic variation within a population

There is a selection pressure that favours a particular phenotype

The phenotype is produced by particular alleles

Individuals with the favoured phenotype are fitter and so more likely to reproduce and
pass on the advantageous alleles to their offspring

Those who do not possess the advantageous allele or phenotype are less likely to
survive and pass on their alleles to their offspring

So over time and several generations the frequency of the advantageous allele
increases and the frequency of other alleles decreases

The Founder effect

The Founder effect occurs when only a small number of individuals from a large parent
population start a new population

As the new population is made up of only a few individuals from the original population only
some of the total alleles from the parent population will be present

In other words, not all of the gene pool is present in the smaller population
A gene pool is the complete range of DNA sequences (alleles) that exist in all the
individuals of a population or species

Which alleles end up in the new founding population is completely up to chance

As a result, the changes in allele frequencies may occur in a different direction for the new
small population vs the larger parent population

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17. Selection & Evolution ⬇

The founder effect in lizards

Anole lizards inhabit most Caribbean Islands and they can travel from one island to another
via floating debris or vegetation

The individual lizards that arrive on an island, as well as the alleles they carry, is
completely up to chance

They may only carry a small selection of alleles, with many more alleles present in the lizard
population on the original island

The lizards on the original island could display a range of scale colours from white to yellow
and the two individual lizards that arrived on the island have white scales
This means that the whole population that grows on that island might only have
individuals with white scales

In comparison, the original island population has a mixture of white and yellow scaled
individuals. This difference between the two populations is completely due to
chance

Genetic drift
When a population is significantly small, chance can affect which alleles get passed onto the
next generation

Over time some alleles can be lost or favoured purely by chance

When there is a gradual change in allele frequencies in a small population due to chance and
not natural selection then genetic drift is occurring

Example of genetic drift in plants

In a small population of five plants growing near a playground with a rubber floor; three of
the plants have blue-and-white flowers and two of the plants have pink-and-white flowers

By chance, most of the seeds from the pink-and-white flowered plants end up on the rubber
floor of the playground, whereas all the seeds from the blue-and-white flowered plants land
on fresh fertile soil where they are able to germinate and grow

Over several generations, the allele for the pink-and-white flowers may disappear from
this population due to chance (because the seeds carrying pink-and-white alleles for flower
colour cannot germinate on rubber)

Bottleneck effect
The bottleneck effect is similar to the Founder effect

It occurs when a previously large population suffers a dramatic fall in numbers

A major environmental event can massively reduce the number of individuals in a population
which in turn reduces the genetic diversity in the population as alleles are lost

The surviving individuals end up breeding and reproducing with close relatives

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17. Selection & Evolution ⬇

Example of the bottleneck effect

A clear example of a genetic bottleneck can be seen in cheetahs today

Roughly 10,000 years ago there was a large and genetically diverse cheetah population

Most of the population was suddenly killed off when the climate changed drastically at
the end of the Ice Age

As a result, the surviving cheetahs were isolated in small populations and lots of
1011891inbreeding occurred

This meant that the cheetah population today has a serious lack of genetic variation

This is problematic for conservation as genetic variation within a species increases the
likelihood that the species is able to respond (survive) in the event of any environmental
changes
Remember the environment exerts a selection pressure on organisms

Processes that cause allele changes table

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17. Selection & Evolution ⬇

17.2.4 NATURAL SELECTION: ANTIBIOTIC RESISTANCE

Natural Selection: Antibiotic Resistance

When humans experience a pathogenic bacterial infection they are often prescribed
antibiotics by a healthcare professional

Antibiotics are chemical substances that inhibit or kill bacterial cells with little or no harm
to human tissue
Antibiotics are derived from naturally occurring substances that are harmful to
prokaryotic cells (structurally or physiologically) but usually do not affect eukaryotic
cells

The aim of antibiotic use is to aid the body’s immune system in fighting a bacterial
infection

Penicillin is a well-known example; it was the first antibiotic to be discovered in 1928 by Sir
Alexander Fleming

Antibiotics are either described as being bactericidal (they kill) or bacteriostatic (they
inhibit growth processes), they target prokaryotic features but can affect both pathogenic
and mutualistic bacteria living on or in the body

However, like in all species, there exists genetic diversity within populations, and the same
applies to disease-causing bacteria

Individual bacterial cells may possess alleles that confer resistance to the effects of the
antibiotic
These alleles are generated through random mutation and are not caused by
antibiotic use, but antibiotic use exerts selection pressures that can result in the
increase in their frequency

Bacteria have a single loop of DNA with only one copy of each gene so when a new allele
arises it is immediately displayed in the phenotype

When an antibiotic is present:

Individuals with the allele for antibiotic resistance have a massive selective
advantage so they are more likely to survive, reproduce and pass genome (including
resistance alleles)

Those without alleles are less likely to die and reproduce

Over several generations, the entire population of bacteria may be antibiotic-

resistant

Antibiotic resistance is an important example of natural selection

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17. Selection & Evolution ⬇

Staphylococcus
There are known populations of the bacterium Staphylococcus that possess alleles which
make them resistant to the effects of penicillin
These are known as resistant strains

Due to the rapid reproduction rate of bacteria (generations of 20-30 minutes for some
species in optimal conditions) a single resistant bacterium can produce 10 000 million
resistant descendants within a day

The future of antibiotic resistance

Antibiotic-resistant strains are a major problem in human medicine

New resistant strains are constantly emerging due to the overuse of antibiotics
By using antibiotics frequently, humans exert a selective pressure on the bacteria,
which supports the evolution of antibiotic resistance

Scientists are trying hard to find new antibiotics that bacteria have not yet been exposed
to, but this process is expensive and time-consuming

Some strains of bacteria can be resistant to multiple antibiotics and they create
infections and diseases which are very difficult to treat

When antibiotics were discovered, scientists thought they would be able to eradicate
bacterial infections, but less than a century later a future is being imagined where many
bacterial infections cannot be treated with current medicines

Exam Tip

Bacteria pass on alleles for antibiotic resistance through reproduction (vertical

gene transfer) but they can also do it in another way.
Bacterium possess plasmids which are a small circular piece of DNA that is
not the main chromosome. Alleles for antibiotic resistance are often found on
these plasmids. Plasmids can be easily transferred from one bacterium
to another, even between different species. This is an example of horizontal
gene transfer.
This means that alleles for antibiotic resistance can be passed one from
species of bacteria to another species.

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17. Selection & Evolution ⬇

17.2.5 NATURAL SELECTION: HARDY-WEINBERG PRINCIPLE

Natural Selection: Hardy-Weinberg Principle

The Hardy-Weinberg principle states that if certain conditions are met then the allele
frequencies of a gene within a population will not change from one generation to
the next

There are seven conditions or assumptions that must be met for the Hardy-Weinberg
principle to hold true

The Hardy-Weinberg equation allows for the calculation of allele and genotype
frequencies within populations

It also allows for predictions to be made about how these frequencies will change in future
generations

Conditions for the Hardy-Weinberg principle

Organisms are diploid

Organisms reproduce by sexual reproduction only

There is no overlap between generations

Mating is random

The population is infinitely large

There is no migration, mutation or selection

Allele frequencies are equal in both sexes

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17. Selection & Evolution ⬇

Hardy-Weinberg equations
If the phenotype of a trait in a population is determined by a single gene with only two alleles
(we will use B / b as examples throughout this section), then the population will consist of
individuals with three possible genotypes:
Homozygous dominant (BB)

Heterozygous (Bb)

Homozygous recessive (bb)

When using the Hardy-Weinberg equations the frequency of a genotype is represented as

a proportion of the population
For example, the BB genotype could be 0.40

Whole population = 1

The letter p represents the frequency of the dominant allele (B)

The letter q represents the frequency of the recessive allele (b)

As there are only two alleles at a single gene locus for this phenotypic trait in the population:

p+q=1

The chance of an individual being homozygous dominant is p2

In this instance, the offspring would inherit dominant alleles from both parents ( p x p

= p2 )

The chance of an individual being heterozygous is 2pq

Offspring could inherit a dominant allele from the father and a recessive allele from
the mother ( p x q ) or offspring could inherit a dominant allele from the mother and
a recessive allele from the father ( p x q ) = 2pq

The chance of an individual being homozygous recessive is q2

In this instance, the offspring would inherit recessive alleles from both parents ( q x

q = q2 )

As these are all the possible genotypes of individuals in the population the following equation
can be constructed:

p2 + q2 + 2pq = 1

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17. Selection & Evolution ⬇

Worked example: Calculating frequencies of genotypes

In a population of birds, 10% of the individuals exhibit the recessive phenotype of white
feathers.

Calculate the frequencies of all genotypes.

Solution:

We will use F / f to represent dominant and recessive alleles for feather colour

Those with the recessive phenotype must have the homozygous recessive genotype, ff

Therefore q2 = 0.10 (as 10% of the individuals have the recessive phenotype and q2
represents this)

To calculate the frequencies of the homozygous dominant ( p2 ) and heterozygous ( 2pq ):

Step 1: Find q:

Step 2: Find p (the frequency of the dominant allele F). If q = 0.32, and p + q = 1 then:

p+q=1

p = 1 – 0.32

p = 0.68

Step 3: Find p2 (the frequency of homozygous dominant genotype):

0.682 = 0.46

p2 = 0.46

Step 4: Find 2pq = 2 x (p) x (q):

2 x (0.68) x (0.32) = 0.44

Step 5: Check calculations by substituting the values for the three frequencies into the
equation; they should add up to 1:

p2 + 2pq + q2 = 1

0.46 + 0.44 + 0.10 = 1

In summary:

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17. Selection & Evolution ⬇

Allele frequencies:
p = F = 0.68

q = f = 0.32

Genotype frequencies:

p2 = FF = 0.46

q2 = ff = 0.10

2pq = Ff = 0.44

Exam Tip

When you are using Hardy-Weinberg equations, start your calculations

determining the proportion of individuals that display the recessive
phenotype – you will always know the genotype for this: homozygous
recessive. Remember that the dominant phenotype is seen in both
homozygous dominant, and heterozygous individuals.
Also, don’t mix up the Hardy-Weinberg equations with the Hardy-
Weinberg principle. The equations are used to estimate the allele and
genotype frequencies in a population. The principle suggests that there is
an equilibrium between allele frequencies and there is no change in this
between generations.

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17. Selection & Evolution ⬇

17.2.6 ARTIFICIAL SELECTION

Artificial Selection

Artificial selection is the process by which humans choose organisms with desirable traits
and selectively breed them together to enhance the expression of these desirable traits over
time and many generations

This practice is also known as selective breeding

Humans have been selectively breeding organisms for thousands of years, long before
scientists understood the genetics behind it

Knowledge of the alleles that contribute to the expression of the desired traits are not
required as individuals are selected by their phenotypes, and not their genotypes
As the genetics is not always understood, breeders can accidentally enhance other traits
that are genetically linked to the desirable trait
These other traits can sometimes negatively affect the organism’s health

Examples of artificial selection include:

Increased milk yield from cattle

Faster racehorses

Disease-resistant crops

There are always biological limitations to how extreme a trait can become in an organism

Principles of selective breeding

1. The population shows phenotypic variation – there are individuals with different
phenotypes / traits

2. Breeder selects an individual with the desired phenotype

3. Another individual with the desired phenotype is selected. The two selected individuals
should not be closely related to each other

4. The two selected individuals are bred together

5. The offspring produced reach maturity and are then tested for the desirable trait.
Those that display the desired phenotype to the greatest degree are selected for further
breeding

6. The process continues for many generations: the best individuals from the offspring are
chosen for breeding until all offspring display the desirable trait

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17. Selection & Evolution ⬇

Artificial selection in racing horses

Selective breeding has been a major part of the horseracing industry for many years.
Breeders have found that horses tend to have one of the three following phenotypes:
Good at sprinting short distances

Good endurance over long distances

All-rounder

If a breeder wanted to breed a horse for a sprinting event they are likely to do the following:
Select the fastest sprinting female horse they have

Select the fastest sprinting male horse they have

Breed the two selected horses

Allow their offspring to reach maturity and test their sprinting speeds to find the
fastest horse (male or female)

The breeder could then use this horse for racing, or they could continue the process
of selective breeding by breeding this horse with another horse that is fast or
descended from fast-sprinters

Over several generations, it would be hoped that the offspring are all fast-sprinters
(but remember there are biological limitations to this)

Exam Tip

Selective breeding can be used to enhance a single desired trait but it can
also be used to combine several desired traits together in a single
individual. A lot of this type of selective breeding is seen in plants. Farmers
are constantly trying to breed plants with a high yield, disease resistance and
the ability to grow in poor soil.

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YOUR NOTES
17. Selection & Evolution ⬇

17.2.7 EXAMPLES OF ARTIFICIAL SELECTION

Examples of Selective Breeding

Selective breeding (or artificial selection) is the process by which humans choose
individuals with desired traits to reproduce, with the aim of producing offspring with the
desired traits also

Most selective breeding is done with the aim of increasing the yield of a sellable product

It is not done with the organism’s survival in mind, and unlike natural selection, it can lead to
organisms that are poorly adapted to their environments

Unless the genetic mechanism behind a trait is fully understood, is highly likely that other
traits could also be accidentally enhanced
Some examples of selective breeding in agriculture and livestock include:
Disease-resistance in wheat and rice varieties

Hybridization in maize

Milk yield in cattle

Disease-resistance in wheat & rice

Wheat plants have been selectively bred for hundreds of years as a crop

Wheat crops can be badly affected by fungal diseases: Fusarium is a fungus that causes
“head blight” in wheat plants

Fungal diseases are highly problematic for farmers as they destroy the wheat plant and
reduce crop yield

By using selective breeding to introduce a fungus-resistant allele from another species of

wheat, the hybrid wheat plants are not susceptible to infection, and so yield increases
Introducing the allele into the crop population can take many generations and
collaboration with researchers and plant breeders

Rice is another crop that has been subject to large amounts of selective breeding

Rice plants are prone to different bacterial and fungal diseases

Examples include “bacterial blight” and “rice blast” caused by the Magnaporthe
fungus

These diseases all reduce the yield of the crop as they damage infected plants

Scientists are currently working hard to create varieties of rice plants that are resistant to
several bacterial and fungal diseases

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17. Selection & Evolution ⬇

Inbreeding & hybridization in maize

Maize (also known as corn) is a staple crop in many countries around the world; it is grown to
feed both livestock and people

In the past, maize plants have been heavily inbred (bred with plants with similar genotypes
to their own)

This has resulted in small and weaker maize plants that have less vigour

This is inbreeding depression which:

Increases the chance of harmful recessive alleles combining in an individual and
being expressed in the phenotype

Increases homozygosity in individuals (paired alleles at loci are identical)

Leads to decreased growth and survivability

A farmer can prevent inbreeding depression by outbreeding

This involves breeding individuals that are not closely related

Outbreeding produces taller and healthier maize plants

It decreases the chance of harmful recessive alleles combining in an individual and

being expressed in the phenotype

Increases heterozygosity (paired alleles at loci are different)

Leads to increased growth and survivability (known as hybrid vigour)

Crops of these plants have a greater yield

Uniformity is important when growing a crop:

If outbreeding is carried out completely randomly, it can produce too much
variation between plants within one field

A farmer needs the plants to ripen at the same time and be of a similar height; the
more variation there is, the less likely this is

In order to achieve heterozygosity and uniformity, farmers buy sets of homozygous seeds
from specialised companies and cross them to produce an F1 generation

Different hybrids of maize are constantly being created and tested for desirables traits
such as: resistance to pests / disease, higher yields and good growth in poor conditions

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17. Selection & Evolution ⬇

Exam Tip

In selective breeding, selection pressure is applied by humans who desire

certain traits in animals or plants – this is why it’s described as artificial
selection.
In natural selection, the environment applies selection pressure on
populations / species – but not to achieve a desirable outcome. Selection
pressures in natural selection are simply driven by the environment in which
organisms live and which features within a population or species are best
suited (adapted) to that environment.

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17. Selection & Evolution ⬇

17.3 EVOLUTION

17.3.1 THEORY OF EVOLUTION

Theory of Evolution

A species can be defined as a group of organisms that are able to interbreed and produce
fertile offspring

Members of one species are reproductively isolated from members of another species

In reality, it is quite hard to define ‘species’ and the determination of whether two organisms
belong to the same species is dependent on investigation

Individuals of the same species have similar behavioural, morphological (structural) and
physiological (metabolic) features

A common example used to illustrate this concept are mules; the infertile offspring produced
when a male donkey and a female horse mate

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17. Selection & Evolution ⬇

The gene pool

The phenotype of all organisms is dependent on its genotype and environmental influence on
this

Members of the same species will have the same genes, of which there may exist alleles
(alternate versions)

A gene pool is the collection of genes within an interbreeding population

A gene pool can be thought of as the sum of all the alleles at all of the loci within the genes
of a population of a single species or a population

The gene pool (or allele frequencies) in a species population can change over time due to
processes such as:
Natural selection

Genetic drift

The founder effect

When the gene pool within a species population changes sufficiently over time, the
characteristics of the species will also change

The change can become so great that a new species forms

This is evolution

Evolution is the formation of new species from pre-existing species over time, as a result
of changes to gene pools from generation to generation

In order for evolution to occur the new species population must be genetically and
reproductively isolated from the pre-existing species population
When this happens, there can no longer be an exchange of genes between the two
populations

Reproductive isolation can occur for a number of reasons, such as when a population splits
and geographical separation (isolation) occurs, preventing mixing, or the incompatibility of
gametes

The evolution of a new species can take a very long time and many generations
For organisms with a short generation time (such as bacteria), evolution can be observed far
more quickly

Genetic isolation
Two groups, when reproductively isolated from each other, become genetically isolated

If two groups are no longer reproducing with each other, then they do not interchange
genes with each other in the production of offspring

Changes that occur in the allele frequencies of each group are not shared, so they evolve
independently of each other which can lead to the formation of two groups that are no
longer successfully able to interbreed

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17. Selection & Evolution ⬇

Evidence of Evolutionary Relationships in DNA

DNA found in the nucleus, mitochondria and chloroplasts of cells can be sequenced and used
to show evolutionary relationships between species

The differences between the nucleotide sequences (DNA) of different species can
provide a lot of information:
The more similar the sequence the more closely related the species are

Two groups of organisms with very similar DNA will have separated into separate
species more recently than two groups with less similarity in their DNA sequences

DNA sequence analysis and comparison can also be used to create family trees that show the
evolutionary relationships between species

DNA Analysis and Comparison

DNA is extracted from the nuclei of cells taken from an organism
DNA can be extracted from blood or skin samples from living organisms or from fossils

The extracted DNA is processed, analysed and the base sequence is obtained

The base sequence is compared to that of other organisms to determine evolutionary

relationships
The more similarities there are in the DNA base sequence, the more closely related (in
that the less distant the species separation) members of different species are

In 2005, the chimpanzee genome was sequenced, and when compared to the human
genome it was discovered that humans and chimpanzees share almost 99% of their DNA
sequences, making them our closest living relatives
In 2012, the sequencing of the bonobo genome also revealed that humans and
bonobos also share 98% of their genome (with slight differences to the differences
seen in chimpanzees)

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17. Selection & Evolution ⬇

Mitochondrial DNA
When analysing DNA from the mitochondria is is important to remember that:
A zygote only contains the mitochondria of the egg and none from the sperm so only
maternal mitochondrial DNA is present in a zygote

There is no crossing over that occurs in mtDNA so the base sequence can only
change by mutation

The lack of crossing over in mtDNA has allowed scientists to research the origins of species,
genetic drift and migration events

It has even been possible to estimate how long ago the first human lived and where
Mitochondrial Eve is thought to have lived in Africa ~200,000 years ago

The estimation of this date relies on the molecular clock theory which assumes
there is a constant rate of mutation over time

The greater the number of differences there are between nucleotide sequences, the
longer ago the common ancestor of both species existed

The molecular clock is calibrated by using fossils and carbon dating

A fossil of a known species is carbon-dated to estimate how long ago that organism
lived

This mtDNA of this species is then used as a baseline for comparison with the
mtDNA of other species

Although for your exams you should say that only maternal mitochondrial DNA can be passed
on or inherited by the zygote, recent research suggests that paternal mDNA may also be
present in zygotes

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17. Selection & Evolution ⬇

17.3.2 ALLOPATRIC & SYMPATRIC SPECIATION

Allopatric & Sympatric Speciation

Evolution causes speciation: the formation of new species from pre-existing species over
time, as a result of changes to gene pools from generation to generation

Genetic isolation between the new population and the pre-existing species population is
necessary for speciation

There are two different situations when speciation can take place:
Two groups of a species are separated by a geographic barrier

Two groups of species are reproductively isolated but still living in the same area
(experiencing similar environmental selection pressures)

Allopatric Speciation
Allopatric speciation occurs as a result of geographical isolation

It is the most common type of speciation

A species population splits into one or more groups which then become separated from each
other by geographical barriers
The barrier could be natural like a body of water, or a mountain range

It can also be man-made (like a motorway)

This separation creates two populations of the same species who are isolated from each
other, and as a result, no genetic exchange can occur between them

If there is sufficient selection pressure or genetic drift acting to change the gene pools
within both populations then eventually these populations will diverge and form separate
species
The changes in the alleles/genes of each population will affect the phenotypes
present in both populations

Over time, the two populations may begin to differ physiologically, behaviourally and
morphologically (structurally)

Example of Allopatric Speciation in Trees

Imagine there is a population of trees that are all one species

A new mountain range forms that divides the population into two

The natural barrier prevents the two groups from interbreeding, so there is no gene flow
between them

The two populations experience different selection pressures and genetic drift

Over thousands of years the divided populations form two distinct species that can no
longer interbreed

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17. Selection & Evolution ⬇

Sympatric Speciation
Sympatric speciation takes place with no geographical barrier
A group of the same species could be living in the same place but in order for speciation to
take place there must exist two populations within that group and no gene flow occurs
between them

Something has to happen that splits or separates the population:

Ecological separation: Populations are separated because they live in different
environments within the same area
For example, soil pH can differ greatly in different areas. Soil pH has a major
effect on plant growth and flowering

Behavioural separation: Populations are separated because they have different

behaviours
For example differences in feeding, communication or social behaviour

Example of Sympatric Speciation in Fish

A species of fish lives in a lake

Some individuals within the population feed on the bottom while others remain higher up in
the open water

The different feeding behaviours separates the population into different environments
Behavioural separation leads to ecological separation

The separated groups experience different selection pressures

Long jaws are advantageous for bottom-feeding whereas shorter jaws are
advantageous for mid-water feeding

Over time natural selection causes the populations to diverge and evolve different
courtship displays

They can no longer interbreed; they are separate species

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17. Selection & Evolution ⬇

Exam Tip

When looking at cases of sympatric speciation try not to confuse the factors
that originally caused a separation between the populations vs the factors
that then prevent them from breeding after genetic isolation. For the
example of the fish: the difference in feeding behaviour is what originally
causes separation but it is a difference in courtship displays (which is caused
by genetic isolation) that prevents them breeding them together.
Also do not forget that speciation is reliant on mutation! Without mutation,
there are no new alleles or genes for selection to act on. The change in
genetic material by mutation is important as it is what produces the
differences in physiology, behaviour and morphology between species.

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18. Classification, Biodiversity & Conservation ⬇

CONTENTS
18.1 Classification
18.1.1 Definitions of Species

18.1.2 The Three Domains: Archaea, Bacteria & Eukarya

18.1.3 Eukarya

18.1.4 Kingdoms

18.1.5 Viruses

18.2 Biodiversity
18.2.1 Ecosystems & Niches

18.2.2 Biodiversity

18.2.3 Random Sampling

18.2.4 Testing for Distribution & Abundance

18.2.5 Pearson's Linear Correlation

18.2.6 Spearman's Rank Correlation

18.2.7 Simpson's Index

18.3 Conservation
18.3.1 Reasons for Extinction

18.3.2 Reasons for Maintaining Biodiversity

18.3.3 Methods of Conservation

18.3.4 Assisted Reproduction

18.3.5 Controlling Invasive Species

18.3.6 Role of IUCN in Conservation

18.1 CLASSIFICATION

18.1.1 DEFINITIONS OF SPECIES

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18. Classification, Biodiversity & Conservation ⬇

Definitions of Species

Scientists have been classifying organisms into species for hundreds of years, in order to
investigate the diversity of life that exists today and in the past

There is difficulty in determining whether new organisms discovered belong to an existing

species, or a new one

This is because the most widely accepted definition of a species is:

A group of organisms with similar morphological and physiological features that
able to breed together and produce fertile offspring

This is the biological species concept, and is reliant on determining whether interbreeding
produces fertile offspring – this is difficult and time-consuming to determine in practice

However there are other discriminating factors that scientists can use to group similar
organisms together

Morphological species concept

In the past, most scientists described organisms by their physical features (morphology) as
these can be more easily observed

They group together organisms that share many physical features that distinguish
them from other species

This is the morphological species concept

Ecological species concept

When there is a population of similar organisms living in the same area at the same
time, they can be described as an ecological species

This is the ecological species concept

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18. Classification, Biodiversity & Conservation ⬇

Naming species
Species are often given common names, but in order to avoid confusion about what group of
organisms scientists are talking about, all species are given a two-part scientific name using
the binomial system

This naming convention was developed and established by the Swedish scientist Carl
Linnaeus in the 18th Century

The first part of the name is the genus that the species belongs to; this is a group of very
similar organisms

The second part of the name is specific and unique to a single group of organisms that are
identified as a species (and occasionally there may be a third name)

The binomial name is always italicized in writing (or underlined if it is not possible to italicise)

For example:
The most commonly known yeast is Saccharomyces cerevisiae

It is common to abbreviate the genus name: S. cerevisiae

Saccharomyces paradoxus is another species of that is a member of the same

genus as cerevisiae

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18. Classification, Biodiversity & Conservation ⬇

18.1.2 THE THREE DOMAINS: ARCHAEA, BACTERIA & EUKARYA

The Three Domains: Archaea, Bacteria & Eukarya

Taxonomy is the practice of biological classification

It involves placing organisms into a series of categories or taxa

By grouping organisms into taxa it can make them easier to understand and remember

There are several different ranks or levels within the hierarchical classification system used
in biology

The highest rank is the domain

Cell type has a major role in the classification of organisms into the three domains; but do
not confuse cell types and domain
Prokaryotic cells are easily distinguishable in that they lack a nucleus

Eukaryotic cells have compartmentalised structures, with at least their genetic

material segregated from the rest of the cell in a nucleus

Based upon molecular analysis of RNA genes in particular, scientists have realised that using
cell type to classify organisms is insufficient, and that prokaryotes could be divided into two
separate groups (domains)

The three domains are:

Archaea (prokaryotes)

Bacteria (prokaryotes)

Eukarya (eukaryotes)

Archaea
Organisms within this domain are sometimes referred to as the extremophile prokaryotes,
archaea were first discovered living in extreme environments, but not all archaea do

Archael cells have no nucleus (and so are prokaryotic)

They were initially classified as bacteria until several unique properties were discovered that
separated them from known bacteria, including:
Unique lipids being found in the membranes of their cells

No peptidoglycan in their cell walls

Ribosomal structure (particularly that of the small subunit) are more similar to the
eukaryotic ribosome than that of the bacteria

Archaea a similar size range as bacteria (and in many ways metabolism is similar between
the two groups)

DNA transcription is more similar to that of eukaryotes

Example: Halobacterium salinarum are a species of the archaea domain that can be found in
environments with high salt concentrations like the Dead Sea

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18. Classification, Biodiversity & Conservation ⬇

Bacteria
These are organisms that have prokaryotic cells which contain no nucleus

They vary in size over a wide range: the smallest are bigger than the largest known-viruses
and the largest are smaller that the smallest known single-celled eukaryotes

Bacterial cells divide by binary fission

Example: Staphylococcus pneumoniae is a bacteria species that causes pneumonia

Eukarya
Organisms that have eukaryotic cells with nuclei and membrane-bound organelles are
placed in this domain

They vary massively in size from single-celled organisms several micrometres across to large
multicellular organisms many-metres in size, such as blue whales

Eukaryotic cells divide by mitosis

Eukaryotes can reproduce sexually or asexually

Example: Canis lupus also known as wolves

Exam Tip

It might be worth refreshing your knowledge on the defining features of

prokaryotic and eukaryotic cells before tackling this new topic!

Differences between Archaea & Bacteria

Domains are the highest taxonomic rank that exist within the hierarchical classification
system of organisms

Initially, all organisms within the Archaea domain were classified as Bacteria

Then several unique features possessed by Archaea were discovered that separated them
from both Bacteria and Eukarya

The main differences between Archaea and Bacteria are seen in:
Membrane lipids

Ribosomal RNA

Cell wall composition

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18. Classification, Biodiversity & Conservation ⬇

Membrane lipids
The membrane lipids found in the cells of Archaea organisms are completely unique

They are not found in any bacterial or eukaryotic cells

The membrane lipids of Archaea consist of branched hydrocarbon chains bonded to glycerol
by ether linkages

The membrane lipids of Bacteria consist of unbranched hydrocarbon chains bonded to

glycerol by ester linkages

Ribosomal RNA
Both Archaea and Bacteria possess 70S ribosomes

The 70S ribosomes in Archaea possess a smaller subunit that is more similar to the
subunit found in Eukaryotic ribosomes than subunits in Bacterial ribosomes
The base sequences of ribosomal RNA in Archaea show more similarity to the
rRNA of Eukarya than Bacteria

The primary structure of ribosome proteins in Archaea show more similarity to

the ribosome proteins in Eukarya than Bacteria

Composition of cell walls

Organisms from the Bacteria domain have cells that always possess cell walls with
peptidoglycan

Organisms from the Archaea domain also have cells that always possess cell walls, however
these do not contain peptidoglycan

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18. Classification, Biodiversity & Conservation ⬇

Characteristics & features of the three domains table

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18. Classification, Biodiversity & Conservation ⬇

18.1.3 EUKARYA

Eukarya

The hierarchical classification system of organisms in biology is used to organise and group
similar organisms together so that they can be more easily understood

There are several taxonomic ranks that exist

Species is the lowest taxonomic rank in the system

Similar species can be grouped in a genus

Similar genuses can be grouped in a family

Similar families can be grouped into an order

Similar orders can be grouped into a class

Similar classes can be grouped into a phylum

Similar phyla can be grouped into a kingdom

Similar kingdoms can be grouped into a domain

Domains are the highest taxonomic rank in the system

There are a few different rhymes that exist to help you remember the different ranks in the
taxonomic classification system. You can always make up your own but the one below is
super helpful!

The first letters of all the different ranks below the domains can be remembered as:
Kings Play Chess On Fancy Gold Squares

Kingdom Phylum Class Order Family Genus Species

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18. Classification, Biodiversity & Conservation ⬇

Classification of an organism in the Eukarya domain

Just like the other domains, Eukarya contains the taxonomic hierarchy of kingdom, phylum,
class, order, family, genus and species

A wolf is an example of an organism in the Eukarya domain

It can be classified further into its kingdom, phylum, class, order, genus and species

A wolf belongs to the following taxonomic groups:

Domain: Eukarya

Kingdom: Animalia

Phylum: Chordata

Class: Mammalia

Order: Carnivora

Family: Canidae

Genus: Canis

Species Canis lupus

The Hibiscus rosa-sinensis is another example of of an organism in the eukarya domain

It is a colourful flowering plant

It belongs to the following taxonomic groups:

Domain: Eukarya

Kingdom: Plantae

Phylum: Angiospermae

Class: Dicotyledonae

Order: Malvales

Family: Malvaceae

Genus: Hibiscus

Species: Hibiscus rosa-sinensis

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18. Classification, Biodiversity & Conservation ⬇

A classification table

Exam Tip

The name of a species always consists of two words: the genus and species.
This means when provided with the Latin name of a species you are
automatically provided with information about the last two taxonomic ranks
that the organism belongs to. Remember this when being asked to show or
explain the classification of an organism in the exam.

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18. Classification, Biodiversity & Conservation ⬇

18.1.4 KINGDOMS

Kingdoms

The domain Eukarya can be divided into 4 kingdoms:

Protoctista

Fungi

Plantae

Animalia

Organisms from each of the four kingdoms have distinct characteristics and features, but
share similarities in that they have cells with membrane-bound nuclei separating genetic
material from the cytoplasm, and compartmentalisation within their cells as a result of the
presence of other organelles

Kingdom Protoctista
All Protoctista are eukaryotic, and this broad group of cellular life encompasses all
eukaryotic cells that do not belong to the other three eukaryotic kingdoms

Members of this kingdom show great diversity in all aspects of life including structure, life
cycle, feeding and trophic levels and well as modes of locomotion

Protoctists can exist as single-celled organisms or as a group of similar cells

A group of Protoctista known as protozoa possess cells similar to animal cells

Their cells have no cell wall

Another group of Protoctista known as algae possess cells similar to plant cells
Their cells have cellulose cell walls and chloroplasts

Stentor roseli is a protoctist that has flagella all over its body which help it feed and move

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18. Classification, Biodiversity & Conservation ⬇

Kingdom Fungi
The oldest organism in the world is thought to be a fungus aged somewhere between 1500 –
10,000 years old

All fungi are eukaryotic cells

The cells of fungi:

Possess non-cellulose cell walls (often made of the polysaccharides chitin and
glucans

Don’t have cilia

Fungi are heterotrophs:

They use organic compounds made by other organisms as their source of energy and
molecules for metabolism

They obtain this energy and carbon by digesting dead/decaying matter

extracellularly or from being parasites on living organisms

Fungi reproduce using spores that disperse onto the ground nearby

Fungi have a simple body form:

They can be unicellular (like the common baker’s yeast Saccharomyces cerevisiae

Some consist of long threads called hyphae that grow from the main fungus body
(mycelium)

Larger fungi possess fruiting bodies that release large numbers of spores

The mould found on bread is actually a fungus: bread mould fungus Rhizopus nigricans

Kingdom Plantae
Plants are multicellular eukaryotic organisms

Plant cells:
All have cell walls composed of cellulose

Possess large (and usually permanent) vacuoles that provide structural support

Are able to differentiate into specialized cells to form tissues and organs

Possess chloroplasts that enable photosynthesis (not all plant cells have
chloroplasts)

Can sometimes have flagella

They are autotrophs

This means they can synthesize their organic compounds and molecules for energy
use and building biomass from inorganic compounds

Plants have complex body forms

They have branching systems above and below the ground

Bristlecone pines are found in the USA, it is estimated that some of them could be 3000 years
old

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18. Classification, Biodiversity & Conservation ⬇

Kingdom Animalia
Animals are also multicellular eukaryotic organisms

Animal cells:
Are able to differentiate into many different specialised cell types that can form
tissues and organs

Have small temporary vacuoles (for example, lysosomes)

Have no cell walls

Sometimes have cilia

They are heterotrophs

They have a wide range of feeding mechanisms

They have a wide range of body forms:

Communication within their complex body forms takes place through a nervous
system and chemical signalling

Blue whales are the largest living animal species

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18. Classification, Biodiversity & Conservation ⬇

18.1.5 VIRUSES

Viruses

Viruses are microorganisms that can only be seen using an electron microscope

They have no cellular structure (and so are acellular and no metabolism

Viruses hijack the DNA replication machinery in host cells

The energy viruses need for replication is provided by respiration in the host cell

Viruses possess none of the characteristic features used for classifying organisms so they sit
outside of the three-domain classification system

There is a wide-ranging debate as to whether viruses should be classified as ‘living’ or ‘non-

living’ based on their inability to carry out the defining features of life outside of a host cell

Classifying viruses by their genetic material

Viruses are classified according to the type of nucleic acid (RNA or DNA) their genome is
made from, and whether it is single-stranded or double-stranded

In cellular organisms like animals and plants, DNA is always double-stranded and RNA
is usually always single-stranded

However, in viruses, DNA and RNA can be either single-stranded or double-stranded

As a result, there are four groups of viruses that exist:

DNA single-stranded viruses

DNA double-stranded viruses

RNA single-stranded viruses (this is the type of genome of SARS-CoV-2, the virus
responsible for the COVID-19 pandemic)

RNA double-stranded viruses

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18. Classification, Biodiversity & Conservation ⬇

Classification of viruses table

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18. Classification, Biodiversity & Conservation ⬇

18.2 BIODIVERSITY

18.2.1 ECOSYSTEMS & NICHES

Ecosystem & Niches

Ecosystems
Speciesdo not exist by themselves in their own isolated environment, they interact with
other species forming communities

These communities interact with each other and the environment they live in, forming
ecosystems

An ecosystem is a relatively self-contained community of interacting organisms and the

environment they live in, and interact with

There is a flow of energy within an ecosystem and nutrients within it are recycled

There are both living (biotic) components and non-living (abiotic)components within an
ecosystem

Ecosystems vary greatly in size and scale

Both a small pond in a back garden and the open ocean could be described as
ecosystems

A human being could also be described as an ecosystem; there are thousands of

species of bacteria living on and in every person

Ecosystems vary in complexity:

A desert is a relatively simple ecosystem

A tropical rainforest is a very complex ecosystem

No ecosystem is completely self-contained as organisms from one ecosystem are often linked
to organisms from another
For example, birds are able to fly long distances to feed from multiple ecosystem

Example of an ecosystem

A forest is a perfect example of a complex ecosystem. There is a large community of organisms

including trees, birds, small and large mammals, insects and fungi. The non-living components of the
ecosystem include: the soil, dead leaves, water from the rain and streams, the rocks and any other
physical or chemical factors. The non-living components of the ecosystem influence the community
of organisms.

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18. Classification, Biodiversity & Conservation ⬇

Niche
The place where a species lives within an ecosystem is its habitat

The role that species plays within an ecosystem is its niche

It encompasses where in the environment the organism is, how it gets its energy
and how it interacts with other species and its physical environment

This is how an organism fits into the ecosystem

Example of a niche

A dung beetle occupies a very specific niche within its ecosystem. Dung beetles have learned to
exploit the dung of animals as a resource and they have a characteristic behaviour of rolling the
dung into balls before transporting it to their underground burrow for storage as food. Their
behaviour within their ecosystem has many knock-on effects on the environment and other
organisms living in it. The burrows and tunnels that they create turns over and aerates the soil and
the buried dung releases nutrients into the soil both of which can benefit other organisms like plants.
The transportation of the dung underground by the beetles also helps to keep fly populations under
control.

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18. Classification, Biodiversity & Conservation ⬇

18.2.2 BIODIVERSITY

Biodiversity

Biodiversity can be thought of as a study of all the variation that exists within and between
all forms of life

Biodiversity looks at the range and variety of genes, species and habitats within a particular
region

It can be assessed at three different levels:

The number and range of different ecosystems and habitats

The number of species and their relative abundance

The genetic variation within each species

Biodiversity is very important for the resilience of ecosystems, in that it allows them to
resist changes in the environment

Ecosystem or habitat diversity

This is the range of different ecosystems or habitats within a particular area or region

If there is a large number of different habitats within an area, then that area has high
biodiversity
A good example of this is a coral reef. They are very complex with lots of
microhabitats and Error: you must enter a valid popover post ID to be exploited

If there is only one or two different habitats then an area has low biodiversity
Large sandy deserts typically have very low biodiversity as the conditions are
basically the same throughout the whole area

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18. Classification, Biodiversity & Conservation ⬇

Species diversity
An ecosystem such as a tropical rainforest that has a very high number of different species
would be described as species-rich
Species richness is the number of species within an ecosystem

Species diversity looks at the number of different species in an ecosystem, and also the
evenness of abundance across the different species present
The greater the number of species in an ecosystem, and the more evenly distributed
the number of organisms are among each species, then the greater the species
diversity

For example, an ecosystem can have a large number of different species but for some
species, there may only be 3 or 4 individuals. As a result, this ecosystem does not
necessarily have high species diversity

Ecosystems with high species diversity are usually more stable than those with lower
species diversity as they are more resilient to environmental changes
For example in the Pine forests of Florida, the ecosystem is dominated by one or
two tree species. If a pathogen comes along that targets one of the two dominant
species of trees, then the whole population could be wiped out and the ecosystem it is
a part of could collapse

Genetic diversity
The genetic diversity within a species is the diversity of alleles and genes in the
genome of species

Although individuals of the same species will have the same genes they will not necessarily
have the same alleles for each gene

Genetic diversity is measured by working out the proportion of genes that have more than
one form (allele) and how many possible alleles each gene has

There can be genetic differences or diversity between populations of the same species
This may be because the two populations occupy slightly different ranges in their
habitat and so are subject to slightly different selection pressures that affect the allele
frequencies in their populations

Genetic diversity within a single population has also been observed

This diversity in a species is important as it can help the population adapt to, and
survive, changes in the environment

The changes could be in biotic factors such as new predators, pathogens and
competition with other species

Or the changes could be through abiotic factors like temperature, humidity and
rainfall

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18. Classification, Biodiversity & Conservation ⬇

18.2.3 RANDOM SAMPLING

Random Sampling

Measuring the different levels of biodiversity within an ecosystem can be a tasking job

Finding out which species live in an ecosystem and the size of the populations requires the
identification and cataloguing of all organisms present to build a species list

This is possible for areas that are very small or where the species are very large like trees

However, for larger and more complex ecosystems like rainforests, it is simply impossible to
find, identify and count every organism that exists there

When this is the case different samples of the area can be taken and used to make an
estimate for the total species numbers in the area

Sampling
Sampling is a method of investigating the abundance and distribution of species and
populations

There are two different types of sampling:

Random

Systematic

In random sampling the positions of the sampling points are completely random or due to
chance
This method is beneficial because it means there will be no bias by the person that
is carrying out the sampling that may affect the results

In systematic sampling the positions of the sampling points are chosen by the person
carrying out the sampling
There is a possibility that the person choosing could show bias towards or against
certain areas

Individuals may deliberately place the quadrats in areas with the least species as
these will be easier and quicker to count

This is unrepresentative of the whole area

When a sampling area is reasonably uniform or has no clear pattern to the way the
species are distributed then random sampling is the best choice

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18. Classification, Biodiversity & Conservation ⬇

18.2.4 TESTING FOR DISTRIBUTION & ABUNDANCE

Testing for Distribution & Abundance

The distribution of a species describes how it is spread throughout the ecosystem

The abundance of a species is the number of individuals of that species

The distribution and abundance of a species in an area can be assessed using different
practical methods:
Frame Quadrats

Line and Belt Transects

Mark-release-capture

Frame quadrats
Some ecosystems are very complex with large numbers of different species of different sizes

For the sake of logistics, sampling is often used to estimate the distribution and
abundance of species

When carrying out sampling, square frames called quadrats can be used to mark off the
area being sampled

Quadrats of different sizes can be used depending on what is being measured and what is
most suitable in the space the samples are being made in

Quadrats must be laid randomly in the area to avoid sampling bias

This random sampling can be done by converting the sampling area into a grid
format and labelling each square on the grid with a number

Then a random number generator is used to pick the sample points

Once the quadrat has been laid on the chosen sample point the abundance of all the
different species present can be recorded

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18. Classification, Biodiversity & Conservation ⬇

Results from quadrats

The results from the quadrats can be used to calculate the predicted frequency and density
of a species within an area

Species frequency is the probability that the species will be found within any quadrat in the
sample area
The number of quadrats that the species was present in is divided by the total
number of quadrats and then multiplied by 100

For example, if bluebells were found in 18 out of 50 quadrats the species frequency
would be (18/50) x 100 = 36%

Species density indicates how many individuals of that species there are per unit area
The number of individuals counted across all quadrats is divided by the total area of
all the quadrats

For example, if 107 bluebells were found across 50 quadrats that are 1m2 each the

species density would be 107/50 = 2.14 individuals per m2

It can sometimes be difficult to count individual plants or organisms. When this is the case
percentage cover of the species within the quadrat can be estimated instead
The quadrat is divided into 100 smaller squares. The number of squares the species is
found in is equivalent to its percentage cover in that quadrat

For example, if grass is found in 89 out of 100 squares in the quadrat then it has a
percentage cover of 89%

Line & belt transects

Throughout some areas, there can be changes in the physical conditions
For example, there may be changes in altitude, soil pH or light intensity

When investigating the species distribution in these kinds of areas systematic sampling is
more appropriate

Methods using transects can help show how species distribution changes with the different
physical conditions in the area
A transect is a line represented by a measuring tape, along which sample are taken

For a line transect:

Lay out a measuring tape in a straight line across the sample area

At equal distances along the tape record the identity of the organisms that
touch the line. For example, every 2m

This produces qualitative data

For a belt transect:

Place quadrats at regular intervals along the tape and record the abundance of
each species within each quadrat

This produces quantitative data

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18. Classification, Biodiversity & Conservation ⬇

Mark-release-capture
The methods above are only useful for stationary organisms

Different methods are required for estimating the number of individuals in a population of
mobile animals

The mark-release-capture method is used in conjunction with the Lincoln Index

For a single species in the area:

The first large sample is taken. As many individuals as possible are caught,
counted and marked in a way that won’t affect their survival

They are returned to their habitat and allowed to randomly mix with the rest of the
population

When a sufficient amount of time has passed another large sample is captured

The number of marked and unmarked individuals within the sample are counted

The proportion of marked to unmarked individuals is used to calculate an estimate

of the population size

The formula for the calculation is:

N = n1 x n2 / m2

Where:
N = population estimate

n1 = number of marked individuals released

n2 = number of individuals in the second sample (marked and unmarked)

m2 = number of marked individuals in the second sample

Worked example: Lincoln index with mark-release-recapture

Scientists wanted to investigate the abundance of leafhoppers in a small grassy meadow. They used
sweep nets to catch a large sample of leafhoppers from the meadow. Each insect was marked on
their underside with non-toxic waterproof paint and then released back into the meadow. The
following day another large sample was caught using sweep nets.

No. caught and marked in first sample (n1) = 236

No. caught in second sample (n2) = 244

No. of marked individuals in the second sample (m2) = 71

Using the equation: N = n1 x n2 / m2 = 236 x 244 / 71 = 811

N (estimated population size) = 811

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18. Classification, Biodiversity & Conservation ⬇

Exam Tip

You will be provided with the formula for Lincoln’s index in the exam. You
need to be able to carry out the calculation to estimate population size from
mark-capture-release data, as you could be asked to do this in the exam.

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18. Classification, Biodiversity & Conservation ⬇

18.2.5 PEARSON'S LINEAR CORRELATION

Pearson's Linear Correlation

When recording the abundance and distribution of species in an area different trends may be
observed

Sometimes correlation between two variables can appear in the data

Correlation is an association or relationship between variables

There is a clear distinction between correlation and causation: a correlation does

not necessarily imply a causative relationship

Causation occurs when one variable has an influence or is influenced by, another

There may be a correlation between species; for example, two species always occurring
together

There may be a correlation between a species and an abiotic factor, for example, a
particular plant species and the soil pH

The apparent correlation between variables can be analysed using scatter graphs and
different statistical tests

Correlation between variables

In order to get a broad overview of the correlation between two variables the data points for
both variables can be plotted on a scatter graph

The correlation coefficient (r) indicates the strength of the relationship between variables

Perfect correlation occurs when all of the data points lie on a straight line with a
correlation coefficient of 1 or -1

Correlation can be positive or negative

Positive correlation: as variable A increases, variable B increases

Negative correlation: as variable A increases, variable B decreases

If there is no correlation between variables the correlation coefficient will be 0

The correlation coefficient (r) can be calculated to determine whether a linear relationship
exists between variables and how strong that relationship is

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18. Classification, Biodiversity & Conservation ⬇

Pearson linear correlation

Pearson’s linear correlation is a statistical test that determines whether there is linear
correlation between two variables

The data must:

Be quantitative

Show normal distribution

Method:
Step 1: Create a scatter graph of data gathered and identify if a linear
correlation exists

Step 2: State a null hypothesis

Step 3: Use the following equation to work out Pearson’s correlation

coefficient r

If the correlation coefficient r is close to 1 or -1 then it can be stated that there is a strong
linear correlation between the two variables and the null hypothesis can be rejected

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18. Classification, Biodiversity & Conservation ⬇

Exam Tip

You will be provided with the formula for Pearson’s linear correlation in the
exam. You need to be able to carry out the calculation to test for correlation,
as you could be asked to do this in the exam. You should understand when it
is appropriate to use the different statistical tests that crop up in this topic,
and the conditions in which each is valid.

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18. Classification, Biodiversity & Conservation ⬇

18.2.6 SPEARMAN'S RANK CORRELATION

Spearman's Rank Correlation

If there is an apparent relationship between two variables but the data does not show a
normal distribution, Pearson’s linear correlation coefficient should not be used

Spearman’s rank correlation determines whether there is correlation between variables

that don’t show a normal distribution

Method:
Step 1: Create a scatter graph and identify possible linear correlation

Step 2: State a null hypothesis

Step 3: Use the following equation to work out Spearman’s rank correlation
coefficient r

Where:
rs = spearman’s rank coefficient

D = difference in rank

n = number of samples

Step 4: Refer to a table that relates critical values of rs to levels of probability

If the value calculated for Spearman’s rank is greater than the critical value for the number of
samples in the data ( n ) at the 0.05 probability level (p), then the null hypothesis can be
rejected, meaning there is a correlation between two variables

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18. Classification, Biodiversity & Conservation ⬇

Exam Tip

You will be provided with the formula for Spearman’s rank correlation in the
exam. You need to be able to carry out the calculation to test for correlation,
as you could be asked to do this in the exam. You should understand when it
is appropriate to use the different statistical tests that crop up in this topic,
and the conditions in which each is valid.
Correlation does not always mean causation. Just because there is a
correlation between the abundance of species A and species B it does not
mean that the presence of species A causes the presence of species B.

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18. Classification, Biodiversity & Conservation ⬇

18.2.7 SIMPSON'S INDEX

Simpson's Index

Once the abundance of different species in an area has been recorded the results can be
used to calculate the species diversity or biodiversity for that area

Species diversity looks at the number of different species in an area but also the evenness
of abundance across the different species

Simpson’s index of diversity (D) can be used to quantify the biodiversity of an area

Simpson’s index
The formula is:

Where:
n = total no. of organisms for a single species

N = total no. of organisms for all species

To calculate Simpson’s Index:

Step 1: First step is to calculate n / N for each species

Step 2: Square each of these values

Step 3: Add them together and subtract the total from 1

The possible values of D are significant:

The value of D can fall between 0 and 1

Values near 1 indicate high levels of biodiversity

Values near 0 indicate low levels of biodiversity

Exam Tip

Remember, you will be provided with the formula for Simpson’s Index in the
exam. You need to be able to carry out the calculation to test for correlation,
as you could be asked to do this in the exam. This also means you should
understand when it is appropriate to use the different statistical tests, and the
conditions in which each is valid.

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18. Classification, Biodiversity & Conservation ⬇

18.3 CONSERVATION

18.3.1 REASONS FOR EXTINCTION

Reasons for Extinction

Extinction is when a species comes to an end or dies out

Extinction is a natural biological process that happens on planet earth and studies of fossils
and ancient DNA have shown that million of species have gone extinct in the past

Mass extinction events have also occurred in the past where a very large number of
species went extinct at one time
The rate of extinction during these periods are very high

Past mass extinctions were likely caused by major and sudden shifts in the environment
such as an Ice Age or an asteroid hitting the earth

Scientists have been studying the current rates of extinction in recent years and many
believe that the earth is undergoing a current mass extinction with humans being the
main cause

Possible reasons for extinction include:

Climate change

Competition

Introduction of species

Hunting by Humans

Degradation and loss of habitats

Climate change
The large scale burning of fossil fuels by humans in recent years has led to a large increase
in the levels of carbon dioxide in the atmosphere, creating the greenhouse effect

The increased carbon dioxide concentration in the atmosphere has had several knock-on
effects on ecosystems around the world
There has been an increase in the mean global temperature

Sea levels are rising

Ocean temperatures and acidity are rising

Ice caps are melting

These knock-on effects have massively changed the habitats of some species, so much
so that some are no longer able to survive in the new environmental conditions
For example, polar bears are struggling to survive as more of their habitat melts away
earlier each year. The earlier melting of the ice caps means they have to swim further
to reach seal populations that they hunt for food

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18. Classification, Biodiversity & Conservation ⬇

Competition
When there is a limited supply of resources within an area competition between
individuals for the same resource can occur

The resources could be food, water, habitat and reproductive mates

Competition can exist within species and between species

Competition reduces the population size of a species

For example, millions of years ago there were many different species of wild dog that
lived in North America. When several cat species spread from Asia into North America
there were high levels of competition between these carnivores. As a result, there are
only nine species of wild dog that exist in North America today

Competition with humans has become a major problem for some species in the last 100
years as humans have taken their food, water and habitat

Introduction of species
When humans colonised new land they would often exchange animal and plant species
between their home country and the new land
These introduced species are non-native

Non-native species can be highly problematic as they often have no natural

competitors, predators or pathogens that help limit population growth

Without these natural population checks, non-native species can massively increase
in number

The large numbers of non-native species can negatively affect the native species
through factors such as competition and disease

Grey squirrels have led to the decimation of the red squirrel population in the UK
Grey squirrels were introduced to the UK in 1876

They quickly grew in numbers

The larger grey squirrels compete with red squirrels for food

They also carry and transmit a disease known as squirrelpox which is fatal to red
squirrels

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18. Classification, Biodiversity & Conservation ⬇

Hunting by humans
In the past humans would have hunted, killed and ate wild animal species in order to survive

Nowadays most of the meat that humans consume comes from domesticated livestock like
cattle, sheep and chicken

The evolution of livestock has negated the need for many humans to hunt wild animals
Some humans in underdeveloped countries still have to hunt animals for survival

The hunting of wild animals is still common and has become a sport for some individuals
The rarer and more vulnerable species are often more desirable for a sport
hunter

If too many individuals within a species are killed then the population can become so small
that it is no longer able to survive

Degradation & loss of habitats

This is the main cause of species extinction

Over recent years humans have aggressively destroyed animals habitats by cutting
down forests, draining wetlands and polluting the water, soil and air

This is highly problematic as species are adapted to survive within their specific
habitat that has particular environmental conditions

Without their habitat organisms will not get the resources they need to survive

As their habitat area gets reduced a species will:

Search for other suitable habitats

Compete with others for the remaining habitat

Eventually the range of habitat can become so small or non-existent that a species is not
able to survive and goes extinct

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18. Classification, Biodiversity & Conservation ⬇

Exam Tip

All of the factors above explain how the population of a species can
dramatically decrease and become very small. It is worth thinking about why
small populations are so much more vulnerable to extinction.
Several things are happening at the genetic level. A smaller population has
increased levels of inbreeding, which reduces the genetic variation in
the population. Genetic drift has a larger impact on a small population
leading to an even further decrease in genetic variation. As we know
from natural selection genetic variation is important as it allows a species to
adapt and survive environmental change; it improves its fitness. So a small
population has a lower fitness meaning increased mortality and decreased
reproduction.

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18. Classification, Biodiversity & Conservation ⬇

18.3.2 REASONS FOR MAINTAINING BIODIVERSITY

Reasons for Maintaining Biodiversity

Biodiversity is the range and variety of genes, species and habitats within a particular
region

It is made up of three components:

Genetic diversity

Species diversity

Ecosystem diversity

Global biodiversity has a major impact on humans and all other species on the planet
There are many reasons for maintaining biodiversity:

1. Moral and ethical

2. Ecological

3. Environmental

4. Economic

5. Aesthetic

6. Agricultural

Moral & ethical reasons

Many people believe that humans have a moral obligation to prevent the manmade loss of
biodiversity

Humans share the planet with millions of others species and they have no right to cause
the extinction of other species

As humans are the most intelligent species on the planet the responsibility falls upon their
shoulders to protect and value all of the organisms on the planet

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18. Classification, Biodiversity & Conservation ⬇

Ecological reasons
Biodiversity has a major effect on the stability of an ecosystem
A more diverse ecosystem is better able to survive and adapt to
environmental changes or threats

For example, if the temperature of a species-rich lake rises due to global warming:
Some species of fish in the ecosystem are unable to cope with the change while
others can

The fish that are able to cope will survive, reproduce and keep contributing to the
ecosystem

Within communities there are keystone species that have a larger impact on the
ecosystem than others

When these species are lost there are several knock-on effects

Bush elephants in the African savannah are a keystone species

They graze in a very extreme way, knocking over and eating several species of tree

This destruction of vegetation actually helps to maintain the ecosystem

Elephant dung also provides a habitat for many important fungi and insect species

When elephants were legally hunted for their ivory, their numbers reduced and
scientists observed a major negative impact on the savannah

Environmental reasons
Humans need diverse ecosystems because of the essential environmental services they
provide

Plants absorb carbon dioxide from the atmosphere and help to reduce the greenhouse
effect and climate change

Microorganisms digest and break down the masses of organic waste that are produced by
larger organisms

Humans have irrigation and drinking water thanks to the transpiration of plants and their
contribution to the water cycle

Different fungi and bacteria species are a major part of the nutrient cycle that allows for
nutrients to reenter the soil for further plant growth

Plants are producers in food webs. They are both a direct and indirect energy source for
humans through fruit, vegetables and meat

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18. Classification, Biodiversity & Conservation ⬇

Economic reasons
Ecosystems have a lot of economic value

Many of the medicines used today have originated from plants, fungi and bacteria
For example the cancer-fighting drug paclitaxel is sourced from Pacific and Himalayan
Yew Trees

The Himalayan Yew has declined in numbers due to over-harvesting for fuel and
medicine

Due to the large number of drugs that have already been sourced from nature it is
reasonable to assume that there are other drugs, yet to be found in nature, that could
be used in the future

Ecotourism a major source of income for many countries

Many tourists travel to and spend money in National parks so they can see wildlife

Increased tourism in a country contributes to the economy and provides jobs

Ecosystems have also made major contributions to the field of science and technology
The specific enzyme used in DNA sequencing was first discovered in thermophilic
bacterium found in a hot spring in Yellowstone National Park, USA

Aesthetic reasons
Humans find great joy and pleasure in the beauty of nature

It provides inspiration for creatives such as photographers, poets, musicians and artists

There is a strong argument for preserving biodiversity because of its aesthetic benefits

Agricultural reasons
Most of the crops that humans grow are very uniform with low genetic diversity

The wild relatives of crops can provide a source of genetic diversity to rescue crops
that are affected by disease or other disasters

Many of the wild relative species are under threat due to habitat destruction and climate
change

All of the world’s potato crop comes from a single species

This lack of species diversity makes the crop highly susceptible to disease

There are over 100 species of wild potatoes that grow in the Andes

These Andean species act as a source of alleles for disease resistance

These alleles have been introduced to the potato crop through gene technology
and interbreeding

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18. Classification, Biodiversity & Conservation ⬇

Summary of reasons for maintaining biodiversity table

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18. Classification, Biodiversity & Conservation ⬇

18.3.3 METHODS OF CONSERVATION

Methods of Conservation

An endangered species is a species that is being threatened with extinction

Conservation of endangered species can be approached in several different ways

Ideally a species should be kept in their natural habitat as all the support systems they
need to maintain life already exist there
National parks and marine parks are examples of conservation methods that do this

When it is not possible to do this endangered species can be captured and placed in
captivity for conservation efforts
Zoos and botanic gardens take part in conservation programmes

Scientists have also come up with several methods to try and ensure the long-term
survival of endangered species through frozen zoos and seed banks

Conserved areas
National parks are areas within countries where the wildlife and environment are
protected

Governments control these areas and pass legislation to ensure their protection

There are several restrictions

Humans access is strictly controlled

Industrial activities such as agriculture and building are tightly regulated

Hunting is limited or completely prohibited

Marine parks are protected areas of water that have been set up for the conservation of
endangered marine ecosystems and species
They also have restrictions to prevent overfishing and pollution

Public engagement with conservation efforts is important for long term success:
National and Marine parks can attract thousands of tourists each year which increases
money and awareness for the conservation effort

Involving members of the local community in the management of protected areas can
provide jobs and increase acceptance of the parks

Some of the profits made from parks can be used to improve the health and
education standards in the nearby communities to illustrate the benefits of having
such areas nearby

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18. Classification, Biodiversity & Conservation ⬇

Galapagos Islands
A large proportion of the land and water surrounding the Galapagos Islands is protected. Humans are
not allowed to travel to many of the islands in the National park and fishing is illegal in the Marine
park areas. Management of these areas is shared between locals and conservation experts. Since it
was established over 50 years ago, there have been strong efforts made to remove invasive species
and increase native species. Rats and goats are captured and removed and the alien plant species
elephant grass is dug up and destroyed while giant tortoises are being reintroduced.

Conservation in captivity
Zoos can also contribute towards the conservation of endangered animal species

Captive breeding programmes can breed individuals of a species so their offspring can be
released into the wild

Zoos are an invaluable resource for scientific research

Scientists are able to closely study animal’s genetics, behaviours and habitat needs

There are some problems with zoos and their role in conservation:
Captive breeding of small species populations can reduce genetic diversity

Certain animal species will not breed in captivity

Not all zoos can provide adequate habitats for animals with specific needs

There are stories of both success and failure when it comes to zoos and conservation:
The oryx is an antelope-like species that was saved from extinction and reintroduced
into the wild in Africa thanks to zoos and captive breeding programmes

Pandas have been in captive breeding programs for over 60 years and not a single
panda has been reintroduced into the wild

Botanic gardens are the plant equivalent of zoos

They use cuttings and seeds collected from the wild to establish a population of the
endangered species in captivity

Methods of tissue culturing and cloning can also be used to obtain large numbers of plants
from a small sample size

The captive population can be used in the future for reintroduction into habitats where they
have become rare

Research is a major role of botanic gardens

They investigate reproduction and growth in different plant species so that they can
be grown in captivity

If the plants original habitat no longer exists they try to find suitable new habitats

Both zoos and botanic gardens are instrumental to education

They help to raise awareness of vulnerable, endangered species and conservation
efforts worldwide

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18. Classification, Biodiversity & Conservation ⬇

Storing genetic material for onservation

If a species becomes extinct in the wild then traditional conservation methods are no longer
useful

New technology has provided ways of storing the genetic material of endangered
species so that it is not lost forever

Frozen zoos store genetic material from animals (eggs, sperm, tissue samples etc) at very
low temperatures so that they can be kept for a very long time
Ideally samples are collected from different individuals of the same species to
maintain the gene pool

The temperature used is roughly -196oC

A large amount of genetic material can be stored in a relatively small space

In the future genetic materials from extinct animal species could be used to breed
and reintroduce a species through IVF and genetic engineering

The San Diego Zoo in the USA has frozen zoo facilities

A seed bank is a facility that conserves plant diversity by drying and storing seeds in a
temperature controlled environment
Usually, seeds of the same species are collected from different sites to maintain the
gene pool

If the plant species goes extinct then the seeds can be used to grow them again

Seeds can only be stored for so long. After a certain period of time the stored seeds
are grown into plants and fresh seeds for storage are taken from those plants

The Svalbard Global Seed Vault in Norway has almost 1 million species of plant
seed. It is located in the Arctic Circle with ideal environmental conditions

Many organisations send seeds from crop plants to be stored there for safekeeping

Some plants have seeds that can not be frozen such as coffee and cocoa plants
In order to preserve the genetic diversity of these plants successive generations must
be grown or tissue cultures taken

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18. Classification, Biodiversity & Conservation ⬇

Summary of conservation of endangered species table

Exam Tip

Remember all of the conservation efforts made to stop a species going extinct
is pointless if they don’t have a natural habitat to return to. Conserving
whole ecosystems is essential for the long term survival of species.
Areas like tropical rainforests and coral reefs have exceptional biodiversity
but they are currently under threat from industrial development, pollution and
exploitation.

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18. Classification, Biodiversity & Conservation ⬇

18.3.4 ASSISTED REPRODUCTION

Assisted Reproduction

Endangered mammals tend to have small and isolated populations

Small populations are prone to inbreeding and inbreeding depression

Inbreeding depression is the reduction in fitness of a population due to breeding
between closely related individuals and the resulting increased homozygosity

When populations are isolated it can also be difficult for individuals to find suitable
reproductive mates

Previously large mammals were transported between zoos in captive breeding programs
Advantage: Humans were able to monitor the health of the mother and foetus
Disadvantage: It was highly expensive and unreliable as sometimes individuals would
refuse to mate

Science has come up with several solutions for inbreeding and the lack of reproductive
mates in endangered mammals

IVF
In vitro fertilization involves the fertilization of an egg outside of the female body
For example in a test tube or petri dish

Method:
A needle is inserted into the female’s ovaries and eggs are extracted

The eggs are kept in a culture medium for a short amount of time

Male semen is mixed with the eggs so fertilization can occur

Several zygotes form and develop into embryos

The embryos are placed in a culture for several days

The embryos are transferred either into the mother, or another female

IVF allows is advantageous over natural mating as it allows humans to control and confirm
fertilization of the embryo

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18. Classification, Biodiversity & Conservation ⬇

Embryo transfer
Pregnancies are high risk for females; complications can arise which in some cases prove
fatal

Since the population numbers of an endangered species are already very low each
reproductive female is of very high value and importance

Embryo transfer can be used to avoid the risks of pregnancy for the vulnerable female
so that she can provide many eggs for multiple offspring

Method:
An egg belonging to a female of the vulnerable species is fertilized by the sperm
belonging to a male of the same species

A zygote forms which develops into an embryo

After fertilization, the embryo is taken from the uterus of the female and
transferred to a surrogate female

The embryo develops to full term and the offspring is born

The surrogate mother can be from another non-vulnerable species

This technique has been used to try and conserve populations of several different species of
African antelope

Surrogacy
A surrogate is any female that becomes pregnant with the embryo from another female
and carries the embryo to full term

Surrogate mothers require hormone treatment before they receive an embryo

The hormones ensure that her uterus is in the right condition for the embryo to
embed

There are multiple ways in which the embryo might have been conceived:
Naturally

Artificial insemination (semen from the male is injected into the uterus of the female)

IVF

A surrogate female can be the same or different species to the biological mother of the
embryo
If it is a different species it needs to be closely related to ensure compatibility of the
embryo and uterus

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18. Classification, Biodiversity & Conservation ⬇

Exam Tip

Sometimes eggs and sperm are frozen so that they can be used at a later
date. Egg cells have a high water content so the internal membranes of eggs
can be damaged by the freezing and thawing process.

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18. Classification, Biodiversity & Conservation ⬇

18.3.5 CONTROLLING INVASIVE SPECIES

Controlling Invasive Species

A species that has moved into an ecosystem where it was previously unknown is an
invasive species

An invasive species can occur naturally as a result of a species migrating or expanding their
habitat but most recorded incidents of invasive species have been caused by humans

In the past humans have:

Knowingly collected and traded species between countries via ships

Unknowingly provided transport for invasive species to a new ecosystem

Introduced alien species deliberately as biological control for pests

Japanese knotweed is the UK’s most invasive non-native plant species

There are several natural population controls that exist for Japanese knotweed in its
natural habitat in Japan. The irregular climate and the deposits of volcanic ash over
the ground limit its growth

A German botanist brought the plant to the UK in the 19th century because he
admired its beauty

As the UK does not possess the same environmental factors the plant was able to
grow unchecked. Since the 1800s it has spread across the UK and become a major
problem

It grows at a rapid rate, breaking up tarmac and blocking out all sunlight for the
native plant species

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18. Classification, Biodiversity & Conservation ⬇

Problems with invasive alien species

The biological process of evolution often brings balance to an ecosystem

Through evolution the environment a species lives in strongly influences the adaptations that
the species evolve to live in that environment

A non-native invasive species will have evolved adaptations for survival in different
environmental conditions so when they are introduced into the new ecosystem this can upset
the balance

In a new ecosystem invasive species will have little or none of the natural population
controls that existed in their previous ecosystem:
They will have no natural predators or competitors

As a result they are able to increase in number at a rapid rate

This can affect the processes within an ecosystem

Competition may occur between invasive species and native species that occupy a
similar with the native species getting displaced or pushed to extinction. It could
be competition for things such as prey, soil nutrients, light and space

Many invasive species can be over successful predators causing a massive decline in
their prey species

Invasive species can introduce new diseases, to which the native species have no
natural

The biodiversity of an ecosystem is negatively impacted which reduces its

productivity

Humans can also feel the knock on effects of an invasive species taking over an ecosystem
The spread of novel diseases and irritants of the skin / respiratory system directly
affect human health

The economy of a country can be severely impacted by the costs of trying to control
invasive species and their negative effects

In the past travel has been brought to a standstill by invasive species, with some
plant species prone to blocking up waterways

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18. Classification, Biodiversity & Conservation ⬇

The cane toad in Australia

In the early 1900s, there was a major problem with the sugarcane crop in Australia. An insect pest
was destroying the crop and causing major economic losses for many farmers. It was decided that
the non-native cane toad (from Hawaii) should be introduced so that it could act as a biological
control. After a short period of time the numbers of cane toads increased rapidly due to a lack of
natural predators and they spread into other habitats outside of the sugarcane plantations. This had
a knock on effect on other species:

The cane toad is toxic when eaten. The northern quoll, which is an endangered marsupial
carnivore, declined steeply in numbers as they preyed on the cane toad

Other amphibian species face increased competition for food and resources

The eggs of ground-nesting birds are often eaten by cane toads

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18. Classification, Biodiversity & Conservation ⬇

18.3.6 ROLE OF IUCN IN CONSERVATION

Role of IUCN & CITES in Conservation

International cooperation is essential if conservation is to be successful

There are several agreements and authorities that exist within and between countries with
the aim of protecting and conserving species worldwide

IUCN
The International Union for the Conservation of Nature (IUCN) is described as “the global
authority on the status of the natural world and the measures needed to safeguard it”

One of the duties that the IUCN carries out is assessing the conservation status of
animal and plant species around the world
The IUCN has their own classification system

There are several different categories and levels that a species can fall into depending
on their population numbers and the threats and risks to those populations

Scientists use data and modelling to estimate which category each species should be
in

Animals that are on the IUCN Red List of Threatened Species™ can be seen online as this
list is made public

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18. Classification, Biodiversity & Conservation ⬇

CITES
The Convention on International Trade in Endangered Species of Wild Flora and Fauna
(CITES) is a global agreement that has been signed by over 150 countries

Its aim is to control the trade of endangered species and their associated products
For example, elephants and their ivory tusks

CITES categorizes endangered and vulnerable species into three appendices:

Appendix I : species that are endangered and face the greatest risk of extinction
(for example, the red panda)

Appendix II: species that are not currently endangered or facing extinction, but
will be unless trade is closely controlled (for example, the venus fly trap)

Appendix III: species included at request of the country that is regulating trade of the
species and trying to prevent its overexploitation (for example, the two-toed sloth
in Costa Rica)

There are different trading regulations that apply to each appendix:

For species in appendix I: all trade in the species and their associated products is
banned

For species in appendix II: trade is only granted if an export permit has been
issued by the involved countries

For species in appendix III: permits are required for regulated trade. Permits are
easier to come by for species in this appendix

Scientists are continuously adding new species and reviewing the status of species already in
the database

There are several concerns about the efficacy of CITES listings

When the trade of a certain endangered species becomes illegal, its price increases

The increased economic value of the species can be a major incentive for people to
break the law

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19. Genetic Technology ⬇

CONTENTS
19.1 Principles of Genetic Technology
19.1.1 Recombinant DNA

19.1.2 Genetic Engineering

19.1.3 Isolating the Desired Gene

19.1.4 Genetic Engineering: Enzymes

19.1.5 Genetic Engineering: Vectors

19.1.6 Genetic Engineering: Promoters & Marker Genes

19.1.7 Gene Editing

19.1.8 Polymerase Chain Reaction

19.1.9 Gel Electrophoresis

19.1.10 Microarrays

19.1.11 Bioinformatics

19.2 Genetic Technology Applied to Medicine

19.2.1 Recombinant Human Proteins

19.2.2 Genetic Screening

19.2.3 Gene Therapy

19.2.4 Gene Technology in Medicine

19.3 Genetically Modified Organisms in Agriculture

19.3.1 Genetically Modified Organisms in Agriculture

19.3.2 Using GMOs in Agriculture

19.1 PRINCIPLES OF GENETIC TECHNOLOGY

19.1.1 RECOMBINANT DNA

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19. Genetic Technology ⬇

Recombinant DNA

The genetic code is universal, meaning that almost every organism uses the same four
nitrogenous bases – A, T, C & G. There are a few exceptions

This means that the same codons code for the same amino acids in all living things
(meaning that genetic information is transferable between species)

Thus scientists have been able to artificially change an organism’s DNA by combining lengths
of nucleotides from different sources (typically the nucleotides are from different species)

The altered DNA, with the introduced nucleotides, is called recombinant DNA (rDNA)

If an organism contains nucleotide sequences from a different species it is called a

transgenic organism

Any organism that has introduced genetic material is a genetically modified organism
(GMO)

Exam Tip

It is because of the universal genetic code that recombinant DNA can be

formed. All forms of life use the same genetic code, which is the strongest
piece of evidence for evolution. Remember, the genetic code is the basis
for storing instructions that, alongside environmental influences, dictate the
behaviour of cells and as a result, the behaviour of the whole organism.

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19. Genetic Technology ⬇

19.1.2 GENETIC ENGINEERING

Genetic Engineering Explained

Genetic engineering is a technique used to deliberately modify a specific characteristic (or

characteristics) of an organism. The technique involves removing a gene (or genes) with
the desired characteristic from one organism and transferring the gene (using a vector)
into another organism where the desired gene is then expressed

The genetically engineered organism will then contain recombinant DNA and will be a
genetically modified organism (GMO)

In order for an organism to be genetically engineered the following steps must be taken:
Identification of the desired gene
Isolation of the desired gene by:
Cutting from a chromosome using enzymes (restriction endonucleases)

Using reverse transcriptase to make a single strand of complementary DNA

(cDNA) from mRNA

Creating the gene artificially using nucleotides

Multiplication of the gene (using polymerase chain reaction – PCR)

Transfer into the organism using a vector (e.g. plasmids, viruses, liposomes)

Identification of the cells with the new gene (by using a marker), which is then
cloned

Genetic engineers need the following to modify an organism:

Enzymes (restriction endonucleases, ligase and reverse transcriptase)

Vectors – used to deliver genes into a cell (eg. plasmids, viruses and liposomes)

Markers – genes that code for identifiable substances that can be tracked (eg. GFP –
green fluorescent protein which fluoresces under UV light or GUS – β-glucuronidase
enzyme which transforms colourless or non-fluorescent substrates into products that
are coloured or fluorescent)

Genetic engineering is being used in the new field of science called synthetic biology
This is an area of research that studies the design and construction of different
biological pathways, organisms and devices, as well as the redesigning of existing
natural biological systems

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19. Genetic Technology ⬇

Exam Tip

In your answer about genetic engineering you should remember to include

the names of the enzymes (restriction endonucleases, reverse
transcriptase, ligase) involved in genetic engineering and mention that
markers (genes which can be identified) and vectors (transfer the desired
gene) are also used.

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19. Genetic Technology ⬇

19.1.3 ISOLATING THE DESIRED GENE

Isolating the Desired Gene

The gene with the specific characteristic that is required can be obtained in the following
ways:
Extracting the gene from the DNA of a donor organism using enzymes (restriction
endonucleases)

Using reverse transcriptase to synthesise a single strand of complementary DNA

(cDNA) from the mRNA of a donor organism

Synthesising the gene artificially using nucleotides

Extraction of gene
The extraction of the gene (containing the desired nucleotide sequence) from the donor
organism occurs using restriction endonucleases

Restriction endonucleases are a class of enzymes found in bacteria. They are used as a
defence mechanism by bacteria against bacteriophages (viruses that infect bacteria, also
known as phages)

The enzymes restrict a viral infection by cutting the viral genetic material into smaller
pieces at specific nucleotide sequences within the molecule. This is why they are called
restriction endonuclease (‘endo’ means within)

They are also referred to as restriction enzymes

There are many different restriction endonucleases because they bind to a specific
restriction site (specific sequences of bases) on DNA, eg. HindIII will always bind to the
base sequence AAGCTT

The restriction endonucleases are named according to the bacteria they are sourced from
and which numbered enzyme it is from that source (eg. HindIII comes from Haemophilus
influenzae and it is the third enzyme from that bacteria)

Restriction endonucleases will separate the two strands of DNA at the specific base sequence
by ‘cutting’ the sugar-phosphate backbone in an uneven way to give sticky ends or straight
across to give blunt ends

Sticky ends result in one strand of the DNA fragment being longer than the other strand

The sticky ends make it easier to insert the desired gene into another organism’s DNA as
they can easily form hydrogen bonds with the complementary base sequences on other
pieces of DNA that have been cut with the same restriction enzyme

When using genes isolated by restriction endonucleases that give blunt ends nucleotides can
be added to create sticky ends

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19. Genetic Technology ⬇

mRNA & reverse transcriptase

Another method to isolate the desired gene is to use the mRNA that was transcribed for that
gene

Once isolated, the mRNA is then combined with a reverse transcriptase enzyme and
nucleotides to create a single strand of complementary DNA (cDNA)

Reverse transcriptase enzymes are sourced from retroviruses and they catalyse the reaction
that reverses transcription. The mRNA is used as a template to make the cDNA

DNA polymerase is then used to convert the single strand of cDNA into a double-stranded
DNA molecule which contains the desired code for the gene

This technique for isolating the desired gene is considered advantageous as it is easier for
scientists to find the gene because specialised cells will make very specific types of mRNA
(eg. β-cells of the pancreas produce many insulin mRNA) and the mRNA (therefore the
cDNA) does not contain introns

Artificial synthesis
As scientists are becoming more familiar with the base sequences for our proteins
(proteome) it is possible to synthesise genes artificially

With the knowledge of the genetic code (that is, which amino acids are required) scientists
use computers to generate the nucleotide sequence (rather than an mRNA template)
to produce the gene

Short fragments of DNA are first produced which are joined to make longer sequences of
nucleotides and then inserted into vectors (eg. plasmids)

This method is being used to create novel genes being used to make vaccines and even to
synthesise new bacteria genomes

Exam Tip

In your answer it is important to include the names of the enzymes

(restriction endonuclease, reverse transcriptase, DNA polymerase)
and the product (cDNA).

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19. Genetic Technology ⬇

19.1.4 GENETIC ENGINEERING: ENZYMES

Genetic Engineering: Enzymes

Genetic engineering is the deliberate modification of a specific characteristic (or

characteristics) of an organism. The technique involves removing a gene (or genes), with
the desired characteristic, from one organism and transferring the gene (using a vector)
into another organism where the desired gene is then expressed

In order to genetically engineer an organism there are a number of enzymes required:

Restriction endonucleases (enzymes) – cuts the DNA strands so that the desired
gene can be isolated or spliced (inserted) into a vector

Reverse transcriptase – reverses transcription to produce a single-strand

complementary DNA (cDNA) from an mRNA strand with the code for the desired gene
DNA polymerase – used to convert the single-stranded cDNA into a double-stranded
DNA molecule of the desired gene

DNA ligase – is used to splice (insert) the gene into the vector

Restriction endonucleases
The role of restriction endonucleases (or restriction enzymes) in the transfer of a gene
into an organism is to:
Isolate the desired gene

Separate the DNA strands (at the same base sequence) in a vector so the desired
gene can be inserted

There are many different restriction endonucleases because they bind to a specific
restriction site (specific sequences of bases) on DNA, eg. HindIII will always bind to the
base sequence AAGCTT

Restriction endonucleases will separate the two strands of DNA at the specific base sequence
by ‘cutting’ the sugar-phosphate backbone in an uneven way to give sticky ends or
straight across to give blunt ends

Sticky ends result in one strand of the DNA fragment being longer than the other strand

The sticky ends make it easier to insert the desired gene into another organism’s DNA or
into a vector as they can easily form hydrogen bonds with the complementary base
sequences on other pieces of DNA that have been cut with the same restriction
endonucleases

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19. Genetic Technology ⬇

Reverse transcriptase
The role of reverse transcriptase in the transfer of a gene into an organism is to produce a
single-strand complementary DNA molecule (cDNA) that contains the code for the
desired characteristic, this will then be inserted into a vector (after being converted into a
double-stranded DNA molecule)

Reverse transcriptase enzymes are sourced from retroviruses and they catalyse the
reaction that reverses transcription. The mRNA (with the genetic code for the desired gene) is
used as a template to synthesise a single strand of complementary DNA (cDNA)

Reverse transcriptase enzymes are often used as it is easier for scientists to find mRNA with
the specific characteristic because specialised cells make very specific types of mRNA (eg. β-
cells of the pancreas produce many insulin mRNA) and mRNA does not contain introns

DNA polymerase
DNA polymerase is used to convert the single strand of cDNA into a double-
stranded DNA molecule which contains the desired code for the gene

The enzyme builds the second strand by pairing free nucleotides with the complementary
bases on the cDNA strand

DNA ligase
DNA ligase catalyses the formation of phosphodiester bonds in the DNA sugar-phosphate
backbone

This enzyme enables the isolated desired gene to be spliced into a vector (generally a
plasmid) so that it can be transferred to the new organism

Exam Tip

It is essential you use the names of these enzymes when you are explaining
genetic engineering. You should also refer to ‘sticky ends’ when discussing
the role of restriction endonucleases. Remember the same restriction
endonuclease must be used in isolating the desired gene and in separating
the DNA in the vector. It is also important to state that the restriction
enzymes cut the DNA or plasmid NOT the gene.

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19. Genetic Technology ⬇

19.1.5 GENETIC ENGINEERING: VECTORS

Genetic Engineering: Vectors

Vectors are used to transfer the desired genes into a foreign cell

Plasmids are the most commonly used vector but viruses and liposomes (a small vesicle with
a phospholipid layer) can also be used to transfer genes

Plasmids
Plasmids are small, circular rings of double-stranded DNA

They occur naturally in bacteria, but can also been found in archaea and eukaryotic
organisms (eg. yeast and fungi) and can contain genes for antibiotic resistance
Plasmids are used as they can self replicate

A plasmid is used to transfer the desired gene to a new organism

To insert the desired gene into the circular DNA of the plasmid it is ‘cut’ open. The same
restriction endonuclease that was used to isolate the desired gene is used to ‘cut’ open
the plasmid. This results in the plasmid having complementary sticky ends to the sticky
ends on the desired gene fragment

DNA ligase forms phosphodiester bonds between the sugar-phosphate backbone of the DNA
fragment and the plasmid to form a recombinant plasmid (a closed circle of double-
stranded DNA containing the desired gene)

Scientists can modify bacterial plasmids or artificially produce them. One benefit of this is
that the plasmids can have one or more marker genes so that cells that have the
recombinant plasmids can be identified

Plasmids are transferred into host cells (usually bacteria) by a process called
transformation. Only a small proportion of bacteria will become transformed and therefore
markers are used to identify these. Transformation can occur by:
Bathing the plasmids and bacteria in an ice-cold calcium chloride solution and then
briefly incubating at 40°C. This makes the bacteria membrane permeable

Electroporation – where the bacteria is given a small electrical shock making the
membranes very porous (this technique can be used to get DNA fragments into
eukaryotic cells)

Viruses
Viruses are commonly used as vectors in the process of gene therapy, which is currently
used to treat genetic diseases such as cystic fibrosis

The viruses are genetically modified to carry non-mutated genes into host cells

Different types of viruses have been used; retroviruses, lentiviruses and adeno-associated
viruses

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19. Genetic Technology ⬇

Liposomes
Liposomes are small spherical vesicles with a phospholipid layer

These vesicles can also be used in gene therapy to carry non-mutated genes into host cells

The advantage of using liposomes as a vector is that they can fuse with the cell surface
membrane

Exam Tip

Remember two enzymes are used in the preparation of a plasmid vector –

restriction endonucleases and DNA ligase. Also the same restriction
endonuclease must be used to ‘cut’ open the plasmid as was used to isolate
the desired gene.

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19. Genetic Technology ⬇

19.1.6 GENETIC ENGINEERING: PROMOTERS & MARKER GENES

Genetic Engineering: Promoter

The promoter (an example of a length of non-coding DNA that has a specific function) is the
region of DNA that determines which gene will be expressed. This is because it is the
site where RNA polymerase binds to in order to begin transcription

The promoter also ensures that RNA polymerase can recognise which is the DNA template
strand. RNA polymerase recognises the template strand as the promoter contains the
transcription start point (the first nucleotide of the gene to be transcribed) which is where the
enzyme will bind

Thus the promoter is used to regulate gene expression because only if it is present will
transcription and therefore the expression of the gene occur
If genetic engineers want to ensure the desired gene is expressed when modifying the
plasmid they have to add an appropriate promoter

As with eukaryotic cells bacteria have many different genes coding for many different
proteins although not all genes are switched on at once. Bacteria will only express genes (to
make proteins) if the growing conditions require a certain protein (eg. coli bacteria only make
β-galactosidase enzymes when their growing medium contains lactose but lacks glucose)

Scientists used this knowledge when first genetically engineering bacteria to produce insulin.
In this case they added the insulin gene along with the β-galactosidase gene to share a
promoter (which switched on the gene when the bacteria needed to metabolise lactose)
So when the scientists grew the bacteria in a medium containing lactose but no
glucose, the bacteria produced the β-galactosidase and human insulin

Genetic Engineering: Marker Genes

A marker is a gene that is transferred with the desired gene to enable scientists to identify
which cells have been successfully altered and now contain recombinant DNA

Antibiotic-resistant genes were once commonly used as marker genes. Scientists

genetically modified the bacteria so that the plasmid contained the desired gene along with a
specific antibiotic-resistant gene (and promoter) and then grew the bacteria on agar plates
embedded with that antibiotic. The bacteria that contained the recombinant plasmids could
be identified as these were the bacteria that grew

Using antibiotic-resistant genes as marker genes concerns scientists as:

There is a risk that the antibiotic-resistant genes could be accidentally transferred
to other bacteria including pathogenic strains creating pathogenic antibiotic-resistant
bacteria

If the resistance spread to other bacteria this could make antibiotics less effective

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19. Genetic Technology ⬇

The spread of the antibiotic-resistant genes can occur due to the conjugation (the transfer
of genetic material from one bacterium to another) or due to transduction (the transfer of
genetic material from one bacterium to another via a virus)

So genes that express proteins that are fluorescent are now commonly used as markers

The fluorescence is due to the presence of a green fluorescent protein (GFP)

The GFP gene along with the desired gene are linked to a specific promoter and once this
promoter is activated, and the protein is expressed, the recombinant bacteria are detected
when they glow green under exposure to ultraviolet light

The use of fluorescent genes as markers is preferable because:

They are easier to identify (all that is required is the ultraviolet light)

More economical (do not need to grow the bacteria on plates of agar infused with
antibiotics)

No risk of antibiotic resistance being passed onto other bacteria

There are antibiotics that are no longer effective and therefore would not stop any
bacteria from growing

Exam Tip

It is a common question to ask about why fluorescent proteins are being used
as markers more often than antibiotic resistance, so ensure you have an
understanding of both methods of identifying the recombinant cells.

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19. Genetic Technology ⬇

19.1.7 GENE EDITING

Gene Editing

Gene genome editing (or editing) allows genetic engineers to alter the DNA of organisms
by inserting, deleting or replacing DNA at specific sites in the genome known to cause
disease. It is a form of genetic engineering where foreign DNA is not introduced into the
genome

Gene editing enables the scientists to be more accurate in their manipulation of the genome.
In the past, inaccurate methods using vectors were used. These included:
Modifying viruses to insert DNA into the gene causing the disease. However this
resulted in DNA being inserted into other genes causing unforeseen consequences

Liposomes (small spheres of lipid molecules) containing the normal gene which was
sprayed into noses. This was only a short-term solution as the epithelial cells lining
the nasal passageway were short lived

Today scientists have developed new gene editing techniques, the most commonly used one
being CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats). This technique
involves using the natural defense mechanism bacteria (and some archaea) have evolved to
cut the DNA strands at a specific point as determined by a guide RNA attached to an enzyme
(Cas9). Once cut scientists can then either insert, delete or replace the ‘faulty’ DNA with
normal DNA

Gene editing is involved in gene therapies (e.g. developing treatments for cystic fibrosis and
sickle cell anaemia). Gene therapy is the treatment of a genetic disease by altering
the person’s genotype

As scientists learn more about the human genome (from the Human Genome Project) and the
proteome, and have the technology to process, large quantities of data through
computational biology, they are gain a better understanding of which genes are responsible
for genetic diseases and where they are located and therefore what base changes need to
occur to treat or cure the disease

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19. Genetic Technology ⬇

19.1.8 POLYMERASE CHAIN REACTION

Polymerase Chain Reaction (PCR)

Polymerase chain reaction (PCR) is a common molecular biology technique used in most
applications of gene technology, for example, DNA profiling (eg. identification of criminals
and determining paternity) or genetic engineering

It is used to produce large quantities of specific fragments of DNA or RNA from very small
quantities (even just one molecule of DNA or RNA). By using PCR scientists can have billions
of identical copies of the DNA or RNA sample within a few hours

The PCR process involves three key stages per cycle. In each cycle the DNA is doubled so
in a standard run of 20 cycles a million DNA molecules are produced. The three stages are
undertaken in a PCR instrument (or thermal cycler) which automatically provides the
optimal temperature for each stage and controls the length of time spent at each stage

Each PCR reaction requires:

Target DNA or RNA being amplified

Primers (forward and reverse) – these are short sequences of single-stranded DNA
that have base sequences complementary to the 3’ end of the DNA or RNA being
copied. They define the region that is to be amplified by identifying to the DNA
polymerase where to begin building the new strands

DNA polymerase – is the enzyme used to build the new DNA or RNA strand. The
most commonly used polymerase is Taq polymerase as it comes from a
thermophilic bacterium Thermus aquaticus which means it does not denature at the
high temperature involved during the first stage of the PCR reaction and secondly,
its optimum temperature is high enough to prevent annealing of the DNA strands that
have not been copied yet

Free nucleotides – used in the construction of the DNA or RNA strands

Buffer solution – to provide the optimum pH for the reactions to occur in

The three stages are:

Denaturation – the double-stranded DNA is heated to 95°C which breaks the
hydrogen bonds that bond the two DNA strands together

Error: you must enter a valid popover post ID – the temperature is decreased to
between 50 – 60°C so that primers (forward and reverse ones) can anneal to the ends
of the single strands of DNA

Elongation / Extension – the temperature is increased to 72°C for at least a minute,

as this is the optimum temperature for Taq polymerase to build the complementary
strands of DNA to produce the new identical double-stranded DNA molecules

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19. Genetic Technology ⬇

Exam Tip

It is important to know the three stages and the temperatures the reactions
occur at during the different stages. You must also know why the Taq
polymerase is used in PCR.

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19. Genetic Technology ⬇

19.1.9 GEL ELECTROPHORESIS

Gel Electrophoresis

Gel electrophoresis is a technique used widely in the analysis of DNA, RNA and proteins.
During electrophoresis the molecules are separated according to their size / mass and
their net (overall) charge

The separation occurs because:

Of the electrical charge molecules carry – positively charged molecules will move
towards the cathode (negative pole) whereas negatively charged molecules will move
towards the anode (positive pole) eg. DNA is negatively charged due to the
phosphate groups and thus when placed in an electric field the molecules move
towards the anode
Different sized molecules move through the gel (agarose for DNA and polyacrylamide
– PAG for proteins) at different rates. The tiny pores in the gel result in smaller
molecules moving quickly, whereas larger molecules move slowly

Of the type of gel – different gels have different sized pores which affects the speed
the molecules can move through them

DNA separation
DNA can be collected from almost anywhere on the body, e.g. the root of a hair or saliva from
a cup. After collection DNA must be prepared for gel electrophoresis so that the DNA can be
sequenced or analysed for genetic profiling (fingerprinting)

To prepare the fragments scientists must first increase (amplify) the number of DNA
molecules by the polymerase chain reaction (PCR). Then restriction endonucleases (enzymes)
are used to cut the DNA into fragments

Different restriction enzymes cut the DNA at different base sequences. Therefore scientists
use enzymes that will cut close to the variable number tandem repeat (VNTR) regions

Variable number tandem repeats (VNTRs) are regions found in the non-coding part of
DNA. They contain variable numbers of repeated DNA sequences and are known to
vary between different people (except for identical twins). These VNTR may be referred
to as ‘satellite’ or ‘microsatellite’ DNA

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To separate the DNA fragments in gel electrophoresis the scientists :

Create an agarose gel plate in a tank. Wells (a series of groves) are cut into the gel at
one end

Submerge the gel in an electrolyte solution (a salt solution that conducts electricity) in
the tank

Load (insert) the fragments into the wells using a micropipette

Apply an electrical current to the tank. The negative electrode must be connected to
the end of the plate with the wells as the DNA fragments will then move towards the
anode (positive pole) due to the attraction between the negatively charged
phosphates of DNA and the anode

The smaller mass / shorter pieces of DNA fragments will move faster and further from
the wells than the larger fragments

The fragments are not visible so must be transferred onto absorbent paper or
nitrocellulose which is then heated to separate the two DNA strands. Probes are then
added, after which an X-ray image is taken or UV-light is shone onto the paper
producing a pattern of bands which is generally compared to a control fragment of
DNA

Probes are single-stranded DNA sequences that are complementary to the VNTR
regions sought by the scientists. The probes also contain a means by which to be identified.
This can either be:
A radioactive label (eg. a phosphorus isotope) which causes the probes to emit
radiation that makes the X-ray film go dark, creating a pattern of dark bands

A fluorescent stain / dye (eg. ethidium bromide) which fluoresces (shines) when
exposed to ultraviolet (UV) light, creating a pattern of coloured bands

Protein separation
The different amino acids (because of the different R groups) determine the charge of
proteins. The charge of the R groups depends on the pH and therefore buffer solutions are
used during the separation of proteins to keep the pH constant

Gel electrophoresis is used to separate polypeptide chains produced by different alleles eg.
the haemoglobin variants (α-globin, β-globin and the sickle cell anaemia variant of β-globin)

Exam Tip

Remember gel electrophoresis is the separation of molecules according to

their size and charge (negatively charged DNA molecules move to the positive
pole). Examiners like to ask questions about gel electrophoresis.

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19. Genetic Technology ⬇

19.1.10 MICROARRAYS

Microarrays

Microarrays are laboratory tools used to detect the expression of thousands of genes at
the same time and to identify the genes present in an organism’s genome

Microarrays are used in medical diagnosis and treatment (e.g. comparison between healthy
cells and diseased cells to find the characteristics of the disease), biotechnology (eg. in
agriculture to identify insect pests), as well as crime (forensic analysis)

As large numbers of genes can be studied in a short period of time microarrays have been
very valuable to scientists

The microarray consists of a small (usually 2cm2) piece of glass, plastic or silicon (also known
as chips) that have probes attached to a spot (called a gene spot) in a grid pattern. There

can be 10 000 or more spots per cm2

Probes are short lengths of single-stranded DNA (oligonucleotides) or RNA which are
synthesised to be complementary for a specific base sequence (this sequence depends on
the purpose of the microarray)

When a microarray is used to analyse genomes:

DNA is collected from the species going to be compared

Restriction enzymes are used to cut the DNA into fragments

These fragments are denatured to create single-stranded DNA molecules

These DNA fragments are labelled using fluorescent tags (the fragments from the
different sources are tagged different colours, usually red and green)

Once these fragments are mixed together they are then allowed to hybridise with the
probes on the microarray

After a set period of time any DNA that did not hybridise with the probes is washed off

The microarray is then examined using ultraviolet light (which causes the tags to
fluoresce) or scanned (colours are detected by the computer and the information is
analysed and stored)

The presence of the colour indicates where hybridisation has occurred, as the DNA
fragment is complementary to the probe. If red and green fluorescent spots appear
then only one species of DNA has hybridised, however, if the spot is yellow then both
species have hybridised with that DNA fragment, which suggests that both species
have that gene in common

If a spot lacks colour that indicates the gene is not present in either species

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19. Genetic Technology ⬇

When genes are being expressed or are in their active state, many copies of mRNA are
produced by transcription. The corresponding proteins are then produced from these mRNAs
during translation. Thus scientists can indirectly, by assessing the quantity of mRNAs,
determine which genes are being expressed in the cells

Microarrays can be used to detect whether a gene is being expressed (a method used to
research cancerous vs non-cancerous cells) by detecting the quantity of mRNA present

To compare which genes are being expressed using microarrays the following steps
occur:
mRNA is collected from both types of cells and reverse transcriptase is used to
convert mRNA into cDNA

PCR may be used to increase the quantity of cDNA (this occurs for all samples to
remain proportional so a comparison can be made when analysis occurs)

Fluorescent tags are added to the cDNA

The cDNA is then denatured to produce single-stranded DNA

The single-stranded DNA molecules are allowed to hybridise with the probes on the
microarray

When the ultraviolet light is shone on the microarray the spots that fluoresce indicate
that gene was transcribed (expressed) and the intensity of the light emitting from
the spots indicates the quantity of mRNA produced (i.e. how active the gene is). If
the light being emitted is of high intensity then many mRNA were present, while a
low intensity emission indicates few mRNA are present

Exam Tip

The colours of the fluorescent tags (red, green and yellow) indicate whether a
gene is present whereas the intensity of light emitted indicates the level of
gene expression (the more light, the more the gene was being expressed) and
this relates to the quantity of mRNA present.

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19. Genetic Technology ⬇

19.1.11 BIOINFORMATICS

Bioinformatics

The various technologies (eg. microarrays and gene sequencing) being used today to analyse
genes and proteins generate enormous quantities of data

The data being collected ranges from the sequences of genomes, when genes are being
expressed during an organism’s life to the structure (amino acid sequence) and functions of
proteins

To analyse all of this data scientists are using bioinformatics

Bioinformatics is an interdisciplinary science (incorporating biology with computer technology

and statistics) where biological data is collected, organised, manipulated, analysed and
stored

Large databases are created containing information ranging from gene sequences to amino
acid sequences of proteins. The databases are available online and can perform analysis of
the data selected. As this data needs to be accessed and searched software developers play
an important role. Some of the databases that exist are:
The European Molecular Biology Laboratory – Nucleotide sequence database

ArrayExpress – a microarray database with the level and types of mRNA expressed in
different cells

Protein Data Bank at Europe – Protein sequence searches

BLAST (Basic Local Alignment Search Tool) – used by researchers to find similarities
between sequences they are studying with those already in the database

Once a genome is sequenced bioinformatics allows scientists to make comparisons with the
genomes of other organisms using the many databases available. This can help to find the
degree of similarity between organisms which then gives an indication of how closely related
the organisms are and whether there are organisms that could be used in experiments as a
model for humans (eg. the fruit fly Drosophila)

The nematode Caenorhabditis elegans is an animal that has been used as a model organism
for studying the genetics of organ development, neurone development and cell death. It was
the first multicellular organism to have its genome fully sequenced and as it has few cells
(less than 1000) and is transparent it has been a useful model

One of the applications for bioinformatics includes using databases with the genome of
Plasmodium to determine which genes and or proteins could be altered or affected to control
the parasite (eg. finding a vaccine for malaria)

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19. Genetic Technology ⬇

19.2 GENETIC TECHNOLOGY APPLIED TO MEDICINE

19.2.1 RECOMBINANT HUMAN PROTEINS

Recombinant Human Proteins

DNA that has been altered by introducing nucleotides from another source is called
recombinant DNA (rDNA)

If the organism contains nucleotides from a different species it is called a transgenic

organism

Any organism that has introduced genetic material is a genetically modified organism
(GMO)

Recombinant DNA has been used to produce recombinant proteins (RP), thus recombinant
proteins are manipulated forms of the original protein

Recombinant proteins are generated using microorganisms such as bacteria, yeast, or animal
cells in culture. They are used for research purposes and for treatments (eg. diabetes,
cancer, infectious diseases, haemophilia)

Most recombinant human proteins are produced using eukaryotic cells (eg. yeast, or
animal cells in culture) rather than using prokaryotic cells, as these cells will carry out the
post-translational modification (due to presence of Golgi Apparatus and / or enzymes)
that is required to produce a suitable human protein

The advantages of genetic engineering organisms to produce recombinant human proteins

are:
More cost-effective to produce large volumes (i.e. there is an unlimited availability)

Simpler (with regards to using prokaryotic cells)

Faster to produce many proteins

Reliable supply available

The proteins are engineered to be identical to human proteins or have

modifications that are beneficial

It can solve the issue for people who have moral or ethical or religious concerns
against using cow or pork produced proteins

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19. Genetic Technology ⬇

Insulin
In 1982, insulin was the first recombinant human protein to be approved for use in diabetes
treatment

Bacteria plasmids are modified to include the human insulin gene

Restriction endonucleases are used to cut open plasmids and DNA ligase is used to
splice the plasmid and human DNA together

These recombinant plasmids are then inserted into Escherichia coli by transformation (bath
of calcium ions and then heat or electric shock)

Once the transgenic bacteria are identified (by the markers), they are isolated, purified and
placed into fermenters that provide optimal conditions

The transgenic bacteria multiply by binary fission, and express the human protein – insulin,
which is eventually extracted and purified

The advantages for scientists to use recombinant insulin are:

It is identical to human insulin, unless modified to have different properties (eg.
act faster, which is useful for taking immediately after a meal or to act more slowly)

There is a reliable supply available to meet demand (no need to depend on

availability of meat stock)

Fewer ethical, moral or religious concerns (proteins are not extracted from cows
or pigs)

Fewer rejection problems or side effects or allergic reactions

Cheaper to produce in large volumes

That it is useful for people who have animal insulin tolerance

Factor VIII
Factor VIII is a blood-clotting protein that haemophiliacs cannot produce

Kidney and ovary hamster cells have been genetically modified to produce Factor VIII

Once modified these recombinant cells are placed into a fermenter and cultured

Due to the optimal conditions in the fermenter, the hamster cells constantly express Factor
VIII which can then be extracted and purified, and used as an injectable treatment for
haemophilia

The advantages for scientists to use recombinant Factor VIII are:

Fewer ethical, moral or religious concerns (proteins are not extracted from human
blood)

Less risk of transmitting infection (eg. HIV) or disease

Greater production rate

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19. Genetic Technology ⬇

Adenosine deaminase
Adenosine deaminase (ADA) is an enzyme used to treat the inherited condition called
Adenosine Deaminase Deficiency

ADA Deficiency is a common cause of Severe Combined Immunodeficiency (SCID)

This is because the immune system is damaged

The larva of the cabbage looper moth has been genetically modified (using a virus vector) to
produce the enzyme adenosine deaminase so that it can be used as a treatment whilst the
patients wait for gene therapy or when gene therapy is not possible

The advantages for scientists to use recombinant adenosine deaminase are:

Fewer ethical, moral or religious concerns (proteins are not extracted from cows)

Less risk of transmitting infection or disease (from cows)

More reliable production of enzyme

Faster to produce many proteins

Exam Tip

Learn how recombinant human insulin is produced and the advantages of

recombinant human insulin being used to treat diabetes.

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19. Genetic Technology ⬇

19.2.2 GENETIC SCREENING

Genetic Screening

In certain circumstances (eg. in the pregnancy in an older woman, or pregnancy where there
is a family history of a genetic disease) may require individuals to determine if they have a
particular allele present in their genome. This can be determined by genetic screening

Genetic screening can help identify individuals who are carrying an allele at a gene locus for
a particular disorder

Genetic screening is the testing of an embryo, fetus or adult to analyse the DNA

The sample of DNA to be analysed can be obtained by:

Taking tissue samples from adults or embryos produced by in-vitro fertilisation
Chorionic villus sampling or amniocentesis of embryos and fetuses in the uterus

As genetic screening can leave future parents with many questions, genetic counsellors
are available to help. The counsellors will read the results and explain them. Counsellors can
also be seen before screening has occurred. They may discuss the following with the
prospective parents:
The chances of the couple having a child with a certain disease

Termination of the pregnancy

Therapeutic treatments possible for the child

Financial implications of having the child

Effect on existing siblings

Ethical issues

Breast cancer (BRCA1 and BRCA2)

BRCA1 and BRCA2 are genes that produce tumour suppressor proteins and thus they play an
important role in regulating cell growth

Faulty alleles of these particular genes exist which increase the risk of an individual
developing breast and ovarian cancers during their lifetime

Faulty BRCA1 and BRCA2 alleles can be inherited from either parent

The advantages of genetic screening for an adult who has a family history of BRCA1 and
BRCA2 gene mutations are:
That the person may decide to take preventative measures (e.g. by having an
elective mastectomy – breast removal – to reduce the risk of developing cancer)

Screening for breast cancer may begin from an earlier age or more frequently,
and the individual (if female) will have more frequent clinical examinations of the
ovaries

That it enables the person to participate in research and clinical trials

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19. Genetic Technology ⬇

Huntington’s disease
Huntington’s is a progressive (gets worse with time) inherited disease that affects the brain

Signs of the disease typically appear in affected individuals after reaching their 40’s and
include uncontrolled movements, lower cognitive (thinking) ability and emotional
problems

There is no cure for the Huntingdon’s disease, with treatments available only alleviating the
symptoms but not curing it

Huntington’s is an autosomal dominant disease (therefore if the person has an allele for
Huntington’s they will get the disease)

The advantage of genetic screening for Huntington’s is it enables:

People to plan for the future (how they will live and be cared for)

Couples to make informed reproductive decisions (as the risk that their children
may inherit the disease is 50%)

People to participate in research and clinical trials

Cystic fibrosis
Cystic fibrosis is an autosomal recessive genetic disorder that is caused by a mutation of
the gene that codes for a transported protein called CFTR

It is a progressive disease that causes mucus in various organs (lungs, pancreas, lungs) to
become thick and sticky. This is because the faulty CFTR protein no longer transports
chloride ions across the cell plasma membrane and therefore water does not move by
osmosis across the membrane either (the presence of water would normally make the mucus
thinner enabling cilia to remove it)

There is no cure for cystic fibrosis, although there are many different treatments that help
alleviate symptoms. The common cause of death is bacterial infection in the lungs

The advantage of genetic screening for cystic fibrosis is:

It enables couples to make informed reproductive decisions (as both may be
carriers and therefore not display any symptoms)

That people can participate in research and clinical trials

Exam Tip

The common reasons why genetic screening is advantageous are: it allows

couples to make informed reproductive decisions and people can participate
in research and clinical trials.

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YOUR NOTES
19. Genetic Technology ⬇

19.2.3 GENE THERAPY

Gene Therapy

Gene therapy involves using various mechanisms to alter a person’s genetic material to
treat, or cure, diseases

As scientists gain a better understanding of the human genome and therefore the location of
genes that cause genetic disorders, the possibilities of gene therapy being able to replace a
faulty gene, inactivate a faulty gene or insert a new gene are growing

Experimental techniques are being used to treat and research treatments for genetic
diseases such as severe combined immunodeficiency (SCID), Leber congenital
amaurosis – a rare form of blindness, β-thalassaemia and haemophilia B
Most gene therapies are still in the clinical trial stage because scientists are having difficulty
finding delivery systems that can transfer normal alleles into a person’s cells and how to
ensure the gene is correctly expressed once there

Finding an appropriate delivery system has been one of the problems. Vectors are currently
used as the delivery system, with viruses being the most commonly used, but non-viral
vectors are also being researched (eg. liposomes and ‘naked’ DNA)

Viruses (eg. retroviruses and lentiviruses) are the most commonly used vectors as they have
the mechanisms needed to recognise cells, and deliver the genetic material into them

Currently all gene therapies have targeted and been tested on somatic (body) Changes in
genetic material are targeted to specific cells and so will not be inherited by future
generations (as somatic gene therapy does not target the gametes)

Often the effects of changing the somatic cells are short-lived

There are two types of somatic gene therapy:

Ex vivo – the new gene is inserted via a virus vector into the cell outside the body.
Blood or bone marrow cells are extracted and exposed to the virus which inserts the
gene into these cells. These cells are then grown in the laboratory and returned to the
person by an injection into a vein

In vivo – the new gene is inserted via a vector into cells inside the body

There is the potential for new genetic material to be inserted into germ cells (cells involved
in sexual reproduction eg. gametes or an early embryo)

However, this is illegal in humans as any changes made to the genetic material of these cells
is potentially permanent and could therefore be inherited by future generations

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19. Genetic Technology ⬇

Severe combined immunodeficiency (SCID)

Severe combined immunodeficiency (SCID) is caused by the body’s inability to produce
adenosine deaminase (ADA), an enzyme that is key to the functioning of the immune
system. Without this enzyme children can die from common infections and therefore need to
be keep isolated often inside plastic ‘bubbles’

To treat SCID scientists have used ex vivo somatic gene therapy. During this therapy, a
virus transfers a normal allele for ADA into T-lymphocytes removed from the patient and
the cells are then returned via an injection

This is not a permanent cure as the T-lymphocytes are replaced by the body over time and
therefore the patient requires regular transfusions every three to five months to keep their
immune systems functioning

Originally retroviruses were used as the vectors, however these viruses insert their genes
randomly into a host’s genome which means they could insert the gene into another gene or
into a regulatory sequence of a gene (which could result in cancer)

Initial treatments did cause cases of leukaemia in children, so researchers switched to using
lentiviruses or adeno-associated viruses as vectors. Lentiviruses also randomly insert their
genes into the host genome however they can be modified to not replicate, whereas adeno-
associated viruses do not insert their genes into the host genome and therefore the genes
are not passed onto the daughter cells when a cell divides. This is an issue with short-lived
cells like lymphocytes but has not been a problem when used with longer living cells such as
liver cells

Inherited eye diseases

An example of a group of inherited eye diseases that causes blindness due to damage to the
light receptors in the retina are Leber Congenital Amaurosis. It begins to affect children
from birth and by their 20s or 30s the person is totally blind. There is no cure for these
diseases

Using in vivo somatic gene therapy, doctors injected into the retina adeno-associated
viruses that contained the normal alleles of one of the genes that caused damage to the
photoreceptors (there are at least 18 known mutated genes causing this group of diseases).
All patients that have had the injections have shown improvement in their eyesight

Exam Tip

Remember that gene therapy in somatic cells is not permanent, whereas in

germ cells it is.

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YOUR NOTES
19. Genetic Technology ⬇

19.2.4 GENE TECHNOLOGY IN MEDICINE

Social & Ethical Considerations

The use of gene technology (genetic screening and gene therapy) in medicine is becoming
more common

Genetic screening in medicine is being used to:

Allow people with a family history of a genetic disease to have their DNA analysed
to determine if they are at risk

Carry out pre-implantation genetic diagnosis (PGD) – embryos that are created
outside the body (with the IVF procedure) have their DNA analysed, which allows for
embryos that are not carrying a harmful allele that would cause the disease, to be
chosen for implantation

Gene therapy is being used in medicine for introducing corrected copies of genes into
patients with genetic diseases (eg. cystic fibrosis, haemophilia, severe combined
immunodeficiency)

Genetic screening
There are many social and ethical considerations for genetic screening, which include:
Being able to take preventative measures (e.g. elective mastectomy when BRCA1
and BRCA2 are detected) – giving individuals control to prevent illness

Using pre-implantation genetic diagnosis to select embryos that do not carry

faulty disease-causing alleles. This could lead to the fear of ‘‘designer babies’ being
created (this includes creating/choosing embryos with tissue matches to older
siblings). Pre-implantation genetic diagnosis can be carried out during in-vitro
fertilisation (IVF); cells are extracted from the embryo in an embryo biopsy and
genetically screened in order to preselect the embryos without faulty alleles

Using genetic counsellors to help people understand their choices and make
informed decisions (eg. financial costs, whether termination of fetus is appropriate if
quality of life is poor)

Risk of miscarriage (which has emotinal consequences) due to the procedures used
to collect DNA which are not 100% risk-free
Amniocentesis – is used to obtain a sample of amniotic fluid using a
hypodermic needle at 15 to 16 weeks of pregnancy

Chorionic villus sampling – is used to obtain a small sample of the placenta

using a needle between 10 and 13 weeks of pregnancy

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19. Genetic Technology ⬇

Choosing to terminate a pregnancy (therapeutic abortion) because the embryo has a

genetic disorder (eg. Thalassaemia or cystic fibrosis) or even terminating the embryo due to
a minor ‘defect’ that could have seen the child lead an almost normal life

Being able to make informed reproductive decisions (eg. Thalassaemia)

Determining whether it is best to know the risk of having a disease, especially when there
is no cure (eg. Huntington’s)

Deciding at what age screening should begin eg. whether parents should be able to choose
for their children to be screened

The possibility of stigmatization and discrimination. The person may feel stigmatized if
they have the disease or discriminated against by health insurers or employers

Confidentiality of the data collected – who will have the right to view the results obtained

Social & ethical considerations of using gene therapy

The social and ethical considerations of using gene therapy include:
The potential for side effects that could cause death (eg. the children who were
treated for SCID developed leukaemia)

Whether germline gene therapy (the alteration of genes in egg and sperm cells
which results in the alteration being passed onto future generations) should be
allowed – it could be a cure for a disease or it could create long-term side effects

The commercial viability for pharmaceutical companies – if it is a rare disease, the

relative small number of patients may not mean that the companies will make a profit
(eg. Glybera – a gene therapy for lipoprotein lipase deficiency is no longer produced
as there were too few patients)

The expense of treatments as multiple injections of the genes may be required if

the somatic cells are short-lived (eg. severe combined immunodeficiency). This may
make the cost of gene therapy accessible to a limited number of people

The possibility that people will become less accepting of disabilities as they
become less common

Who has the right to determine which genes can be altered and which cannot (eg.
should people be allowed to enhance intelligence or height)

Another method of enhancing sporting performances unfairly through gene doping.

This is where the genes are altered to give an unfair advantage eg. to provide a
source of erythropoietin (the hormone that promotes the formation of red blood cells)

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19. Genetic Technology ⬇

19.3 GENETICALLY MODIFIED ORGANISMS IN AGRICULTURE

19.3.1 GENETICALLY MODIFIED ORGANISMS IN AGRICULTURE

Genetic Engineering: Use in Agriculture

Genetic engineering is a technique used to deliberately modify a specific characteristic (or

characteristics) of an organism

The technique involves removing a gene (or genes) with the desired characteristic from
one organism and transferring the gene (using a vector) into another organism where
the desired gene is then expressed

The genetically engineered organism will then contain recombinant DNA and will be a
genetically modified organism (GMO)

Although plants and animals have been genetically engineered to produce proteins used in
medicine, the main purpose for genetically engineering them is to meet the global demand
for food

Crop plants have been genetically modified to be:

Resistant to herbicides – increases productivity / yield

Resistant to pests – increases productivity / yield

Enriched in vitamins – increases the nutritional value

Farmed animals have been genetically modified to grow faster. It is rarer for animals to be
modified for food production due to ethical concerns associated with this practice

Scientists have genetically modified many organisms including bacteria (eg. to produce
insulin), sheep (eg. to produce a human blood protein known as AAT), maize (eg. to be
resistant to insect attacks), rice (eg. to produce β-carotene to provide vitamin A)

The benefits of using genetic engineering rather than the more traditional selective breeding
techniques to solve the global demand for food are:
Organisms with the desired characteristics are produced more quickly

All organisms will contain the desired characteristic (there is no chance that
recessive allele may arise in the population)

The desired characteristic may come from a different species / kingdom

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19. Genetic Technology ⬇

GM salmon
In 2015 AquaAdventure Salmon was approved by the US Food and Drug Authority (FDA) for
human consumption

This salmon has been genetically modified (GM) to grow more rapidly than non-GM salmon
as a result of growth hormone being produced in the salmon throughout the year, instead of
just in spring and summer. The producer therefore has a product to sell in half the time,
which increases their yield

Scientists combined a growth hormone gene from a chinook salmon with the promoter
gene from an ocean pout, a cold-water fish. The ocean pout fish can grow in near-freezing
waters, thus the promoter gene ensured the growth hormone was continually being
expressed

To prevent the GM salmon from reproducing in the wild, all the salmon are female and sterile

Herbicide resistance in soybean

Growing herbicide-resistant soybeans allows farmers to spray a herbicide on the crop
after germination to kill weeds that would otherwise compete with the growing soybeans for
light, water and minerals, therefore decreasing the yield

The resistant gene comes from a strain of the bacterium Agrobacterium

This gene allows an enzyme in the soybean to continue to synthesise three amino acids
(phenylalanine, tyrosine and tryptophan) needed to produce proteins required in the
growing tips of plants

The herbicide glyphosate inhibits the enzyme in plants without the resistant gene; without
the proteins being synthesised, the plants die

Insect resistance in cotton

Cotton has been genetically modified with a gene for the Bt toxin, which is taken from the
bacterium Bacillus thuringiensis

Cotton plants modified with the Bt toxin gene produce their own insecticide

When an insect ingests parts of the cotton plant, the alkaline conditions in their guts activate
the toxin (the toxin is harmless to vertebrates as their stomach is highly acidic), killing the
insect

Different strains of thuringiensis produce different toxins which are toxic to different insect
species

Insect populations have developed resistance to the genes for Bt toxin, reducing
effectiveness as a means of protecting crops

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19. Genetic Technology ⬇

19.3.2 USING GMOS IN AGRICULTURE

GMOs in Food: Social & Ethical Implications

The genetic modification of microorganisms for the production of medicines, antibiotics and
enzymes raises little debate compared to the use of genetically modified organisms (GMOs)
for food production

The use of GMOs in food production has been proposed as a solution to feeding the
increasing world population, the decreasing arable land and decreasing the impact on the
environment, however concerns such as the development of resistance in insects and weeds
and costs of seeds have meant that countries are not allowing GMOs to be grown

The solution could be integrated pest-management systems that could help avoid the
development of resistance and increased population of secondary pests

Ethical implications
The ethical implications of using GMOs in food production are:
The lack of long-term research on the effects on human health – should GM food be
consumed if it is unknown whether it will cause allergies or be toxic over time
(although there has been no evidence to suggest this would occur to date)

Making choices for others:

That without appropriate labelling the consumer cannot make an informed
decision about the consumption of GM foods

As the pollen from the GM crop may contaminate nearby non-GM crops that
have been certified as organic

By reducing the biodiversity for future generations

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19. Genetic Technology ⬇

Social implications
The social implications of growing GMOs for food evolve around whether the crops are safe
for human consumption and for the surrounding environment

The possible implications are:

The GM crops may become weeds or invade the natural habitats bordering the
farmland

The development of resistance for the introduced genes in the wild relative
populations

Potential ecological effects (e.g. harm to non-targeted species like the Monarch
butterflies)

Cost to farmers (new seed needs to purchase each year)

Could cause allergic reactions

The ability to provide enriched foods to those suffering from deficiencies (eg. Golden
Rice) and therefore decrease in diseases

Reduced impact on the environment due to there being less need to spray pesticides
(eg. less beneficial insects being harmed)

Reduction in biodiversity which could affect food webs

The herbicides that are used on the GM crops could leave toxic residues

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