TABLE OF CONTENTS

2
CHAPTER 1
Biodiversity

5
CHAPTER 2
Classification

7
CHAPTER 3
Conservation

9
CHAPTER 4
Energy and Respiration

13
CHAPTER 5
Photosynthesis

17
CHAPTER 6
Inherited Change

24
CHAPTER 7
Selection and Evolution

28 Homeostasis
CHAPTER 8

32
CHAPTER 9
Coordination

39 Genetic Engineering
CHAPTER 10
 CIE A2-LEVEL BIOLOGY//9700
1. BIODIVERSITY
1.1 Terms
• Species: a group of organisms with similar morphological
and physiological features, which can interbreed to
produce fertile offspring and are reproductively isolated
from other species.
• Ecosystem: a relatively self-contained, interacting
community of organisms, and the environment in which
they live and with which they interact. Consists of biotic
and abiotic parts
• Niche: is the role of an organism in an ecosystem (it is
how an organism fits into the ecosystem).
1.2 Biodiversity
Biodiversity: The variety of species in an area along with
their variation within species and the genetic diversity
between them.
• The three levels of diversity:
o Variation in ecosystems or habitats
o Number of different species in the ecosystem and
their relative abundance
o Genetic variation within each species
• Uses of maintaining biodiversity:
o Maintains stability of ecosystem; preventing extinction
o Maintains large gene pool (genetic variation)
o Ecosystems provide ‘services’ for humans
o Species can be source of new medicines
o Resource such as food and wood
o Leisure for humans to see in zoos; ecotourism
o Climate stability
1.3 Genetic Diversity
• Is the diversity of the alleles within the genes in the
genome of a single species
• A species can all have the same genes, but different
alleles for those genes. Genetic diversity is assessed by
finding proportion of genes with different alleles and
how many alleles there are per gene.
PAGE 2 OF 44
1.4 Species Diversity
• The number of species in a community is known as
species richness
• Species diversity takes species richness into account, but
also includes evenness of abundance of each species
In species diversity there are two points that need to be
found: distribution and abundance of species.
To do this we use means of Random sampling such as:
• Quadrat
• Mark and release
• Simpson’s Index of Biodiversity
The importance of random sampling is that a habitat may
be too large for actual counting so a sample is quick and
gives a representation of the whole habitat.
1.5 Random Sampling
Used when area looks uniform or there’s no clear pattern
of the way species are distributed
Quadrat sampling:
• Decide size of quadrat and number of samples
• Mark a specific area
• Samples are taken randomly eg by using random number
generator to give coordinates of sampling points in the
area to avoid any bias and increase accuracy of estimate
• Take measurement of abundance of specific species
• Note: usually used with species that are stationary
• 2 ways to use your results:
o Species frequency: is the measure of the chance of a
particular species being found in any one quadrant.
𝑁𝑜. 𝑜𝑓 𝐴𝑝𝑝𝑒𝑎𝑟𝑎𝑛𝑐𝑒
× 100
𝑁𝑜. 𝑜𝑓 𝑄𝑢𝑎𝑑𝑟𝑎𝑡𝑠
o Species density: is a measure of how many individuals
there are per unit area.
𝑇𝑜𝑡𝑎𝑙 𝑁𝑜. 𝑜𝑓 𝑖𝑛𝑑𝑖𝑣𝑖𝑑𝑢𝑎𝑙𝑠 𝐶𝑎𝑙𝑐𝑢𝑙𝑎𝑡𝑒𝑑
Units: m-2
𝑇𝑜𝑡𝑎𝑙 𝐴𝑟𝑒𝑎 𝑜𝑓 𝐴𝑙𝑙 𝑄𝑢𝑎𝑑𝑟𝑎𝑡𝑠
▪ When unable to count, use percentage cover
1) Divide eg 100 x 100 cm quadrat to 100 small
squares
2) Decide approx. what % area inside quadrat is
occupied by each species
 CIE A2-LEVEL BIOLOGY//9700
▪ Alternatively, use the Braun-Blanquet abundance Drawing a kite diagram
scale. • Find the highest value from the table e.g. 6 in this case
Mark-release and recapture: • Give each species 6 spaces on y axis
• Used with mobile animals • Draw a straight line of 0 through the middle
o As many individuals possible are caught • Divide the number you are plotting by two, plot it above
o Each individual is marked in a way that would not and below the line (from 0)
affect its chance of survival or reproduction
o The marked individuals are counted and returned to
their habitat to mix randomly
o After enough time elapses for mixing to take place,
capture another sample
o Number of marked and unmarked counted and used
to calculate estimate of population
𝑛1 × 𝑛2
𝑁=
𝑚2
N = population estimate
n1 = number of marked individuals released
n2 = total number of individuals (both marked and 1.7 Correlation
unmarked) captured Correlation coefficient (r): determine whether there is a
m2 = number of marked individuals recaptured linear relationship and its strength (ie how close the points
are to the line)
1.6 Systematic Sampling
• Used to determine species distribution in areas where
conditions such as altitude, soil moisture content, pH or
exposure to light intensity varies
Using transacts: to detect changes in community
composition along a line across one or more habitats.
• Line transect
The number of organisms found at regular points along
a line are noted.
Assume the null hypothesis is true: there is no correlation
between the two samples
Create a scatter graph to see if there’s a correlation
• Belt transect between the abundance of 2 species
The abundance of organisms within quadrats placed at
regular intervals

PAGE 3 OF 44
 CIE A2-LEVEL BIOLOGY//9700
1.7.1 Pearson’s linear correlation 1.7.2 Spearman’s rank correlation
• Interval data that must be distributed normally- you can • Used to find out if there’s a correlation when data is not
see this if the graph does not appear skewed or has normally distributed
obvious outliers 6 × 𝛴𝐷 2
𝑟𝑠 = 1 − ( 3 )
• Must have linear correlation 𝑛 −𝑛
• The two variables can be on either axis 1. Rank both species (where the highest data is
• Quantitate data as measurements or counts ranked 1 and so on)
𝛴𝑥𝑦 − 𝑛𝑥̅ 𝑦̅ 2. Calculate the difference in rank in each quadrat, D
𝑟=
𝑛𝑠𝑥 𝑠𝑦 3. Square the difference
𝑛 = sample size (number of observations) 4. Find the sum of 𝐷 2 , and proceed with formula.
𝑥, 𝑦 = number of species x, number of species y • The closer the value rs is to 1, the more likely it is that
𝑥̅ ,̅𝑦= mean there is a correlation between the two sets of data
𝑠𝑥 , 𝑠𝑦 = standard deviation of x and y • The rs value you calculated is then compared with the
• The value of r is always between -1 and 1, where -1 critical value- if rs is greater than the critical value, then
indicates a negative correlation, 1 indicates positive null hypothesis is rejected, meaning there is a significant
correlation, and 0 indicates no correlation. correlation.
Example Example
Number of Number of n Physics Rank Maths Rank 𝑫 𝐷2
Quadrat species P, species Q, 𝒙𝑦 1 35 3 30 5 2 4
𝒙 𝑦 2 23 5 33 3 2 4
1 10 21 210 3 47 1 45 2 1 1
2 9 20 180 4 17 6 23 6 0 0
3 11 22 242 5 10 7 8 8 1 1
4 7 17 119 6 43 2 49 1 1 1
5 8 16 128
7 9 8 12 7 1 1
6 14 23 322
8 6 9 4 9 0 0
7 10 20 200
9 28 4 31 4 0 0
8 12 24 288
∑𝐷 2 = 12
22 264
9 12 𝑟𝑠 = 0.9
10 9 19 171 • As 𝑟𝑠 = 0.9, it is close to 1 and there is a correlation
mean 𝑥̅ 𝑦̅ Σ𝑥𝑦 between the 2 sets of data.
𝑛𝑥̅ ,̅𝑦 10 × 10.2 × 20.4 = 2080.8 = 2124 Example critical value table at 5% error
Standard n 5 6 7 8 9 10 11
𝑠𝑥 = 2.10 𝑠𝑦 = 2.55 1 1.00 0.89 0.79 0.76 0.68 0.65 0.60
deviation
𝑟 = 0.81 • Critical value at 𝑛 = 9 is 0.68
• Since 𝑟𝑠 > 0.68, there is a significant correlation between
• As 𝑟 = 0.81 it is closer to 1 and is a positive correlation. the data sets.

PAGE 4 OF 44
 CIE A2-LEVEL BIOLOGY//9700
1.8 Simpson’s Index of Diversity 2. CLASSIFICATION
• After abundance of species is calculated in the area you 2.1 Taxonomic Hierarchy
are studying, use this formula to calculate the diversity • Biologists created a process called classification to
𝑛 2
𝐷 =1− 𝛴 (𝑁) arrange organisms into groups; these taxa form a
where n is the total number of organisms of a particular hierarchy which helps group organisms
species, and N is the number of all species
• Value of D ranges from 0 to 1(1 being highly diverse) Dashing
• Advantage: do not have to identify organisms to King
calculate diversity
Phillip
Example
Number of Came
individuals ,n 𝒏 𝟐
Species ( ) Over
𝑵
Shore A
A 24 0.00 For

B 367 0.110 Great

C 192 0.030
D 14 0.000 Spaghetti

E 83 0.006
F 112 0.010
G 207 0.035
H 108 0.010
Total no. of 𝑛 2
1107 𝛴 (𝑁) = 0.201
individuals, N
𝐷 = 1 – 0.201 = 0.799 ∴ high diversity

PAGE 5 OF 44
 CIE A2-LEVEL BIOLOGY//9700
2.2 Domain
Three domains:

Feature Bacteria Archaea Eukarya

Present, with DNA arranged as
No nucleus, DNA exists as circular chromosomes without
Nucleus linear chromosomes with
histones, along with small circular Plasmids
histone proteins
Membrane
No membrane bound organelle Present
bound organelle
70S ribosomes smaller than
70S ribosomes, smaller than eukaryote but have features 80S ribosomes in the cytosol,
Ribosomes
eukaryotic ribosome that are similar to eukaryotic but also has 70S in mito/chloro
ribosome
Cell division Binary fission Mitosis
Always present and contains Always present, but no Present sometimes (cellulose)
Cell wall
peptidoglycan peptidoglycan and has cell membrane
Many forms: unicellular,
Size Usually single cell or small groups of cells colonial(group mutual benefit)
and multicellular
Archaea’s metabolism is similar to that of bacteria, but the way transcription occurs much in
Notes
common with eukarya

2.3 Kingdoms
Protoctista
Eukaryotic
Single cell, or exist as group
of similar cells
Some animal like cells (no
cell wall) → Protozoans
Plant like (cellulose cell
walls and chloroplast) ie
algae
Fungi
Eukaryotic
Do not have chlorophyll so
cannot photosynthesize
Heterotrophic nutrition-
feed as parasites and
getting organic compounds
from other organisms
Reproduce by means of
spores
Cell wall made up of chitin
or other substances
Never have cilia or flagella
Simple body form, can be
unicellular or made up of
long threads of hyphae.
Large form such a
mushrooms produced by
compacted masses of
hyphae ie fruiting bodies
Plantae Animalia
Multicellular, differentiated to form tissues and organs
Specialized cells
Heterotrophic nutrition-
Autotrophic- Some have
rely on others to make
chloroplast and
their food or get their
photosynthesize
energy
Cell vacuoles are small and
Cells have large permanent
temporary like lysosomes
vacuoles
and food vacuoles.
Cell walls always present
No cell walls
and made up of cellulose
May occasionally have Cells sometimes have cilia
flagella or flagella
Communication by nervous
system

PAGE 6 OF 44
 CIE A2-LEVEL BIOLOGY//9700
Viruses are not classified in the 3 domain classes as they
are considered dead (they don’t undergo MRS GREN), also
they do not have any of the features that are used in the
classification.
• Structure only visible by electron microscope
• Acellular- they do not have cellular structure like
bacteria and fungi however they have particles made of
proteins and nucleic acids similar to cellular organisms.
• Infectious but have no metabolism when they are free
• When they infect cells, they use the biochemical
machinery of the host cells to copy their nucleic acids
and make their proteins → destruction of host cell.
• Energy for these processes is obtained by host cells’
respiration
Taxonomic system for viruses:
• Is based on the diseases which they cause
• Type of nucleic acid they contain (DNA or RNA)
• Whether nucleic acid is double/single stranded
Note: in cellular organism’s DNA is double stranded and
RNA is single stranded but in viruses both can be either
single or double.
3. CONSERVATION
3.1 Threats to Biodiversity
Five major threats to biodiversity:
• Habitat loss and degradation of environment
• Climate change
• Excessive use of fertilizers and industrial and domestic
forms of pollution
• Over exploitation and unsustainable use of resources
• Alien species
o Habitat loss: process in which habitat is rendered
functionally unable to support the species present. In
this process, the organisms that previously used the
site are displaced, habitats get divided into smaller
areas (habitat fragmentation) or destroyed, reducing
biodiversity and leading to extinction in extreme cases.
o Deforestation: due to farming, urbanisation etc leads
to severe land degradation as a result of soil erosion.
o Climate change: plants and animals affected as they
may not be able to adjust.
▪ Major cause is greenhouse gas emission from eg
organic waste (methane) and factories (CO2). It traps
more heat, causing global warming and a rise in sea
levels.
PAGE 7 OF 44
▪ As the earth gets warmer, organisms at high altitudes
find it difficult to adapt.
o Acidification/temp rise of the oceans can destroy
aquatic life such as coral reefs, algae and molluscs.
o Coral reefs are an example of key stone species ie
species that play a central role in the ecosystem, and
whose existence effects the entire community. They
have been destroyed due to overfishing, mining,
fertilizer run-off, and high temperatures (leading to
coral bleaching ie when coral becomes white as algae
leaves coral which supply O2 to coral)
o Pollution caused by untreated industrial and domestic
waste leaking into the environment, effecting animals’
metabolism or excretion.
▪ Substances such as polychlorinated biphenyl (PCBs)
enter our food chains, effects our immune systems
and reduces fertility.
o Non-biodegradables such as plastic can be eaten by
turtles.
o Fertilizers can drain into rivers causing eutrophication,
killing all species in that ecosystem.
o Air pollution causes acid rain, affecting aquatic life and
vegetation.
o Over exploitation: hunting and poaching for eg ivory,
and overfishing due to overpopulation
o Alien species: invasive species that moved from one
ecosystem to another by trading animals and used to
control pests.
o Increase in disease: alien species could introduce
diseases
3.2 Why does Biodiversity Matter?
• Moral and ethical: some people/cultures believe we
have no right to cause extinction of other species.
• Ecological: ecosystems are more stable when
biodiversity is high. They also add direct value to us eg
medicinal herbs must be protected so that species
beneficial to us are not lost.
o Nutrient cycles and food chains are disrupted when
biodiversity is harmed.
• Aesthetic: many people enjoy the variety of organisms
and habitats on earth, which provide inspiration for
creative people.
• Social and commercial: animals or plants that are
important to the economy of countries are
interbred/genetically engineered to produce crops that
increase yield and have useful characteristics.
 CIE A2-LEVEL BIOLOGY//9700
o It’s also a source of employment and ecotourism.
o Microorganisms are sources of useful products eg
mass production of Taq polymerase for polymerase
chain reaction by genetically modified bacteria
o Timbre and sandal wood obtained are a source of
income
• Other services:
o Forests maintain CO2 level, reduce flooding and
provide a huge habitat for thousands of organisms
3.3 Protecting Endangered Species
Zoo: has a variety of functions in addition to providing
enjoyment and interest for visitors who can study
animals they would not be able to see otherwise.
• Advantages:
o Provide protection for endangered species and have
successful captive breeding programs with the aim of
reintroducing them to their natural habitat.
o Maintain genetic diversity by breeding with different
mates.
o Research to better understand breeding habits,
habitat requirements and ways to increase genetic
diversity
• Disadvantages:
o Not all conservation attempts are a success
o Animals can refuse to breed in captivity
o Sometimes not possible to create suitable habitat
o Difficult for animals to adapt to wildlife as they were
used to being cared for.
o They do not have the skills required to survive in
natural habitat as they can’t:
▪ Avoid predators
▪ Find food
▪ Rear their own
Frozen zoos & seed banks: storage facility in which
genetic materials taken from animals (e.g. DNA, sperm,
eggs, embryos and live tissue) are gathered and stored
at very low temperatures for optimal preservation over a
long period.
Botanic gardens: similar to zoos for endangered plants.
Seeds or cuttings are collected, cultured and cloned from
species in the wild to increase its population which can
later be introduced in natural habitat.
• Advantages:
o Protect endangered plant species
o Research methods of reproduction and growth, so
they can be grown in appropriate conditions
PAGE 8 OF 44
o Reintroduce species to habitats where they have
become rare/extinct
o Educate public in the roles of plants in our ecosystem
and their economic value
o Contains seed banks: seeds are stored so that if any
plant becomes extinct there would be seeds from
which they can be grown.
▪ Preferably, seeds of the same species is collected
from different sites to maintain gene pool.
▪ Germination tests carried out every 5 years to check
if stored seeds still viable.
• Disadvantages:
o Possibility of altering genetic diversity
o Gene pool decreases esp for small populations as an
even smaller sample is taken for store, which is
unrepresentative of the genetic diversity of the entire
population.
o Some plant seeds are difficult to be dried and frozen.
Conserved areas (national parks and marine parks): set
areas where wildlife and environment have some form
of protection controlled by government, and where
human activity is limited.
o Marine parks: conserve fragile ecosystems at risk of
overfishing, dredging and pollution
• Advantages of conserved areas:
o Strict limits on agriculture, building, mining, fishing,
hunting and other threatening activities
o Restricted access to areas that are sensitive to human
interference
o Alien animal and invasive plant species are removed
o Captive breeding and reintroduction programs
o Money from tourism used to pay for park’s
maintenance, spreading awareness about
conservation, improve local health/education facilities
o Local people employed and given areas of land for
farming
o Animals are not moved from natural environment
o Closer feel to wildlife than zoos
• Disadvantages:
o Threats are still so great that some species have to be
moved from natural habitat and placed somewhere
safer eg zoos
o Animals are restricted in specific area (cannot migrate)
 CIE A2-LEVEL BIOLOGY//9700
3.4 Methods of Assisted Reproduction
Assisted reproduction is a solution to infertility and
inbreeding.
Zoos do not have to transport large mammals between
them for their captive breeding programs as instead, their
sperm is taken and stored in a sperm bank.
• Artificial insemination (AI): sperm is then inserted in the
vagina and into the uterus using a catheter when a
female is ovulating.
o Female may be given hormone to super ovulate
(produce large number of eggs into the oviduct)
• Embryo transfer: is used when the animal is endangered
and cannot be risked with pregnancy, so the embryo is
flushed out and transferred to surrogate mothers.
• In vitro fertilisation (IVF):
o Needle inserted in ovaries to extract mature follicles
which is cultured for some time and then mixed with
semen in vitro.
o Resulting zygote divides to form an embryo which is
cultured for days and then placed into the mother or
surrogate mother.
3.5 Culling and Contraceptives
• Culling: is the process of killing/moving animals from a
breeding stock to control population growth
• Birth control:
o Vasectomy (cutting sperm duct)
o Steroid hormones
o Vaccine which targets layer of glycoprotein around the
egg (zona pellucida). When injected, antibodies attach
to glycoproteins, blocking sperm from fertilizing the
egg - 90% success.
3.6 Non-Governmental Organizations
International conservational organization signed
agreements like:
• Convention on International Trade in Endangered
Species of Wild Flora and Fauna (CITES)
o Agreement signed by 145 countries
o Controls trade in endangered species and products
from them e.g. fur, skin and ivory
o It has appendices which list endangered species
according to set criteria
Species don’t always benefit from this organization as
when a product becomes illegal, then practice to obtain
this product rises.
PAGE 9 OF 44
• WWF - World Wide Fund of Nature
o Campaigning group for wildlife conservation
o Funds conservation projects
o Publicizes environmental issues
o Campaigns to save ecosystems from degradation and
species from extinction
3.7 Restoring degraded habitats
• Conservation involves restoring areas that have been
degraded by human activity or by natural catastrophes
• Small scale e.g. when a farmer decides to plant trees on
land that is no longer needed or has become degraded
by overuse
• e.g. after centuries of deforestation, soil erosion and
severe land degradation in Haiti, efforts are made to
restore forests. About 70% of the countries land is
unsuitable for agriculture. There are numerous tree
planting projects to rescue the agriculture.
• In Cornwall, UK, the Eden project is dedicated to
education people in plant diversity and the need for
conservation.
4. ENERGY AND RESPIRATION
4.1 Energy
Energy is needed for work in living organisms e.g:
• Anabolic reactions: synthesizing complex substances
from its monomers eg protein synthesis and DNA
replication.
• Active transport of substances eg the sodium-potassium
pump.
• Mechanical work eg muscle contraction and cellular
movement such as flagella or cilia.
• Maintaining body temperature (homeostasis).
• Bioluminescence and nerve impulse transmission
• DNA replication
4.2 ATP Adaptation for Universal Energy
Currency
Note: Energy does not come from breaking these bonds,
but from changes in chemical potential energy.
• ATP is readily hydrolysed to release energy
 CIE A2-LEVEL BIOLOGY//9700
• Immediate source of energy • Pyruvate, still contains large amount of chemical
• Small and water soluble; easily transported around cell potential energy therefore if oxygen is available, then
• Pi is a good leaving group, as ATP synthase can efficiently Krebs cycle and oxidative phosphorylation is continued
reattach the Pi to ADP to form ATP (reversible). to make use of this energy.
• Has a high turnover rate Link Reaction
• Links anabolic (energy requiring) and catabolic (energy • Occurs in the matrix of mitochondrion therefore must
yielding) reactions require pyruvate to actively be transported into matrix
• ATP is produced from a variety of reactions • Decarboxylation occurs; which is the removal of CO2
ATP synthesis • Dehydrogenation also occurs: removal of H2
ATP CAN BE SYNTHESIZED BY TWO ROUTES Pyruvate (3C)
Substrate linked Chemiosmosis NAD
Reduced NAD CO2
• Glycolysis • Oxidative
• Krebs cycle phosphorylation & ETC
Acetyl (2C) CoA
Only oxidative phosphorylation requires oxygen as the
• Coenzyme A is a complex molecule composed of
it is needed to combine with electron/proton in the
nucleoside (adenine plus ribose) with Vitamin, it acts as
final acceptor. No ETC would mean no proton gradient
a carrier for acetyl groups (CH3-CO) to the Krebs cycle.
produced ∴ Chemiosmosis (synthesis of ATP) does not
Net Gain • CO2
occur.
• Reduced NAD
4.3 Respiration Note: Remember there is 2 pyruvate molecules formed
in glycolysis so net gain is 2 times
Respiration is the process in which organic molecules act
as a fuel Krebs Cycle
1. Glycolysis Closed pathway of enzyme controlled reactions which also
occurs in the matrix.
2. Link reaction
• Although reaction is part of aerobic respiration, the
3. Krebs cycle oxygen present
reactions make use of no oxygen as it is only necessary
4. Oxidative phosphorylation
for oxidative phosphorylation.
Glycolysis
Is the lysis of glucose to form 2 molecules of pyruvate (3C) • Acetyl (2C) CoA combines with Oxaloacetate (4C) to
which occurs in the cytoplasm of the cell. produce Citrate (6C).
• First stage is phosphorylating glucose using 2 ATP, this is • Citrate is decarboxylated to produce CO2, and
done to provide activation energy for the reaction. dehydrogenated to reduce NAD and FAD.
• Note: during phosphorylation, glucose is first converted • Oxaloacetate is regenerated to continue the cycle.
Acetyl (2C) CoA
to glucose phosphate using ATP, then to its isomer CoA
fructose phosphate without the use of ATP, and finally to
fructose bisphosphate using another ATP.
Oxaloacetate 6C
Reduced NAD NAD
CO2
NAD
Reduced NAD
Reduced
FAD
5C
NAD
FAD

ATP Reduced
NAD CO2
ADP
Net Gain 2 ATP and 2 Reduced NAD
4C
PAGE 10 OF 44
 CIE A2-LEVEL BIOLOGY//9700
• 2CO2
Balance Sheet
• 1 Reduced FAD
Net Gain ATP ATP NET NAD
• 3 Reduced NAD USED MADE ATP REDUCED
• 1 ATP GLYCOLYSIS -2 4 +2 2
Note: Remember there is 2 acetyl CoA molecules so net LINK REACTION 0 0 0 2
gain is 2 times KREBS CYCLE 0 2 +2 6
OXIDATIVE 0 28 +28 0
Oxidative Phosphorylation and the Electron transport PHOSPHORYLATION
chain (ETC) TOTAL -2 34 +32 10
This stage involves chemiosmosis which takes place in the
inner mitochondrial membrane (Cristae)
• 2 FAD is reduced only in the Krebs cycle
• Reduced NAD and FAD are passed to the electron • Reduced FAD and NAD are oxidised in oxidative
transport chain. phosphorylation.
• Reduced NADs and FADs release hydrogen atoms which
then split up into H+ and 1e-. • ATP yield per stage of respiration:
• Electrons move down an energy gradient across the ETC
to release energy.
• This energy is utilised to pump H+ ions from the matrix to
the intermembrane space producing a proton gradient.
• H+ then move down conc. gradient through ATP synthase
back into the matrix via facilitated diffusion.
• ADP + Pi → ATP, also occurs while the protons pass
through ATP synthase. This happens by utilising the
protons’ electrical potential energy for chemiosmosis.
• Oxygen acts as the final e- acceptor to form water.
1/2O2 + 2H+ + 2e- → H2O

Theoretically
• Reduced NAD produces 3 molecules of ATP
• Reduced FAD produces 2 molecules of ATP
However, some energy is used to transport ADP into the
mitochondrion and ATP into the cytoplasm ∴
Realistically
• Reduced NAD produces 2.5 molecules of ATP
• Reduced FAD produces 1.5 molecules of ATP
Net Gain • Most ATP produced is 28 molecules

PAGE 11 OF 44
 CIE A2-LEVEL BIOLOGY//9700
o Oxidation of lactate to Co2 and H20
4.4 Respiration without Oxygen o Reoxygenation of haemoglobin in the blood
• In the absence of oxygen, the final e- is not accepted and o A high metabolic rate, as many organs are operating
hydrogen can’t be disposed of in the ETC. Thus, reduced above resting level.
NAD is not oxidised and the chain stops.
• This produces a small yield of ATP as only glycolysis
occurs
Alcohol fermentation in plants

4.5 Respiratory substrate

• The more hydrogens per molecule a substance has, the
more energy value per unit mass, thus greater energy
density
Carbohydrate Protein Lipid

• This is because most of the energy liberated in

respiration comes from oxidation of hydrogen to water
• Glycolysis takes place normally • To calculate the energy value of a substance, burn a
• Pyruvate is decarboxylated to ethanal known mass with oxygen in a calorimeter
• Ethanal is reduced to ethanol by accepting hydrogen • The energy is determined by the rise in temp of the
from reduced NAD, with the help of enzyme alcohol water
dehydrogenase (this enzyme helps with removal of H
from NADH)
• Reaction cannot be reversed, and remaining chemical
potential energy in ethanol is wasted.
Lactate fermentation in animals

Respiratory quotient (𝑅𝑄): the ratio of oxygen taken in to

carbon dioxide given out.
It is used to show what substrate is being used in
respiration, and whether or not anaerobic respiration is
• Pyruvate is reduced to lactate by the enzyme lactate occurring.
𝑣𝑜𝑙𝑢𝑚𝑒 𝑜𝑓 𝐶𝑂2 𝑔𝑖𝑣𝑒𝑛 𝑜𝑢𝑟 𝑝𝑒𝑟 𝑢𝑛𝑖𝑡 𝑡𝑖𝑚𝑒
dehydrogenase 𝑅𝑄 =
𝑣𝑜𝑙𝑢𝑚𝑒 𝑜𝑓 𝑂2 𝑡𝑎𝑘𝑒𝑛 𝑖𝑛 𝑝𝑒𝑟 𝑢𝑛𝑖𝑡 𝑡𝑖𝑚𝑒
• Reaction is reversible by transporting lactate to the liver,
converting it back to pyruvate
• Oxygen debt: the post exercise uptake of extra oxygen
to pay off oxygen deficiency which is needed for:
o Conversion of lactate to glycogen in the liver

PAGE 12 OF 44
 CIE A2-LEVEL BIOLOGY//9700
RESPIRATORY SUBSTRATE RESPIRATORY QUOTIENT
(RQ)
Carbohydrate 1.0
Lipid 0.7
Protein 0.9
• When values are closer to infinity or higher than 1.0,
anaerobic respiration is occurring, values below 1 shows
aerobic respiration
• No RQ value for muscle cells in anaerobic respiration as
only lactate is produced with no CO2 being produced

4.6 Adaptations of rice for wet fields • Note: this apparatus can also be used to measure RQ
• Can respond to flooding by growing taller, ensuring top where 𝑥 is the oxygen consumption, 𝑦 is the increase of
part of leaves and flower are held above water, allowing volume of air due to CO2 production (fluid falls), and 𝑧 is
oxygen and carbon dioxide to be exchanged via stomata the decrease in volume of air when more O2 is consumed
• Contains loosely packed aerenchyma cells in the cortex than CO2 produced (fluid rises)
of stems allowing oxygen to diffuse into deprived areas • Manometer fluid stays constant when O2 consumption
• Air is trapped in between ridges of underwater leaves and CO2 production are equal (RQ=1)
that have hydrophobic corrugated surfaces to keep air 5. PHOTOSYNTHESIS
within the leaves’ contact
• Can tolerate high levels of ethanol (toxic) by the
production of alcohol dehydrogenase which breaks it
down
• Ethanol stimulates gibberellin, which in turn stimulates
cell division, hence increasing internodal length

4.7 Respirometer
• Measures oxygen uptake in a sealed container for
respiring organisms eg germinating seeds or invertebrate
organism
• CO2 produced is absorbed by soda lime/concentrated
KOH or NaOH.
• The decrease in the volume of air results from their
oxygen consumption and rises the manometer fluid in
the tube.
• Oxygen consumption per unit time can be measured by
reading the level of the manometer fluid against a scale.
• Temperature must be kept constant via thermostatically
controlled water bath.
• A control tube helps maintain pressure – it contains
equal volume of inert material as the volume used in the
experimental tube so that any changes in atmospheric
pressure can be compensated for
• Finally, a graph of oxygen consumption against
temperature can be plotted.
• Chloroplast appear as biconvex discs about 3-10 µm
• Thylakoid membrane: where light-dependent reactions
occur
o Its membrane contains photosystems, inside which
chlorophyll molecules are located.
o It also has accessory pigments, ETC and ATP synthase
• Grana: stacks of thylakoid membranes, increasing
surface area for light dependent reactions. Its
membrane:
o Holds ATP synthase for chemiosmosis
o Allows pigments to be arranged in light harvesting
clusters (in funnel like structures) for efficient light
absorption.
• Stroma: contains enzymes for Calvin cycle (light
independent reactions), 70S ribosomes, circular DNA,
lipid droplets, starch grains
• Starch granule → insoluble storage carbohydrate
product of photosynthesis

PAGE 13 OF 44
 CIE A2-LEVEL BIOLOGY//9700
Adaptation of palisade tissue:
• Contain large numbers of chloroplasts
• Large vacuole helps in pushing chloroplast to edge of cell
for max light absorption and short diffusion pathway
• Chloroplasts can move towards light and away from
intense light to avoid damage
• Elongated & arranged to intercept maximum light
• Closely packed to absorb maximum light
• Large surface area for diffusion of gases
• Moist cell surfaces for diffusion of gases
• Thin cell walls for maximum light penetration and
diffusion of gases
5.1 Light Dependent Stage
• Takes place in the thylakoid membranes
• Photosystems are required to trap wavelengths of light
(photons) to energize the electron found in the primary
pigment (chlorophyll α)
• Photoactivation: the excitation of an e- to a higher
energy level, causing it to escape a chlorophyll molecule
• Accessory pigments are arranged in light harvesting
clusters that pass on absorbed energy to the primary
pigment at reaction centre
• Photosystem I absorbs wavelengths of 700nm
• Photosystem II absorbs wavelengths of 680nm
Non-Cyclic photophosphorylation
PAGE 14 OF 44
1. Accessory pigments in PSII absorb photons of light. The
energy is passed onto primary pigment,
exciting primary pigments e- to a higher energy level and
causing them to escape the photosystem.
o Photolysis: photosystem II contains a water splitting
enzyme that catalyses the lysis of water in the
presence of light:
2𝐻2 𝑂 → 𝑂2 + 4𝐻 + + 4𝑒 −
▪ Oxygen diffuses out of the chloroplast and into the air
▪ The protons build up in the thylakoid lumen causing a
gradient to be formed
▪ The electrons in water replace the electrons that have
left the primary pigment
2. The energized electrons are taken up by electron
acceptors, and are passed down the ETC, which generates
energy to pump protons from stroma to lumen. e- then
travel to PS I, where more light is absorbed by the
chlorophyll molecules and the e- are reenergised.
3. 𝑒 − + 𝐻 + → 𝐻
𝐻 + 𝑁𝐴𝐷𝑃 → 𝑁𝐴𝐷𝑃𝐻
4. The combination of the water splitting and the proton
pumping caused protons to build up inside the thylakoid
lumen, generating a proton gradient across the thylakoid
membrane. ATP is therefore photophosphorylated using
the ATP synthase enzyme in exactly the same way as
respiration.
Cyclic photophosphorylation
• Only involves Photosystem I
• E- is photoactivated and is accepted by e- acceptor
rather than falling back into the photosystem and giving
out thermal energy
• It is then passed on via a chain of electron carriers,
during which, enough energy is released to synthesize
ATP by chemiosmosis
• ATP is then passed on to light independent reactions
• Electron then returns to Photosystem I
 CIE A2-LEVEL BIOLOGY//9700
• Difference between cyclic and non-cyclic 5.3 Limiting Factors
CYCLIC NON-CYCLIC
Only photosystem I Both photosystems
involved involved
e- emitted returns to e- emitted from PSII is
same photosystem absorbed by PSI

Reduced NADP produced

Photolysis of H2O, O2
byproduct
5.2 Light Independent Stage
• Occurs in the stroma of chloroplast and is called the
Calvin Cycle
• 𝐶𝑂2 + 𝑅𝑢𝐵𝑃 + 𝑅𝑢𝑏𝑖𝑠𝑐𝑜 → 𝑢𝑛𝑠𝑡𝑎𝑏𝑙𝑒 6𝐶
6𝐶 → 2 𝑋 𝐺3𝑃 (3𝐶)
• G3P is reduced and activated to form triose phosphate
(TP or PGA). The ATP and NADPH from the light-
dependent reactions is used in this step. The ADP and
NADP return to the thylakoid membrane for recycling
• Most of the triose phosphate regenerates the RuBP
using ATP
o Some of the triose phosphate molecules condense to
hexose phosphates, to in turn form glucose, cellulose,
sucrose and starch.
o Others converted to amino acids, lipids, or acetyl
coenzyme A (CoA).
• Limiting factors: if a process is affected by more than
one factor, the rate will be limited by the factor which is
nearest its lowest value
• Limiting factors of photosynthesis: light intensity,
carbon dioxide concentration and temperature.
• Without enough light, a plant cannot photosynthesise
very quickly, even if there is plenty of water and carbon
dioxide.
• At low light intensities, the limiting factor for rate of
photosynthesis is the light intensity; as the intensities
increase so does the rate. But at high light intensity, one
or more other factors must be limiting, such as
temperature or carbon dioxide supply.
• The effects of limiting factors can be investigated using
aquatic plants such as Elodea or Cabomba.

o The number of bubbles produced in unit time can be

counted in different conditions
o A better method would be to calculate the volume of
gas produced over time

5.4 Glasshouses
• A better understanding of the environmental factors on
rate of photosynthesis allows us to manage the growth
of plants in protected fields increasing yield of crop.
• Sensors monitor light intensity, humidity and
concentration of CO2 and control optimum conditions

PAGE 15 OF 44
 CIE A2-LEVEL BIOLOGY//9700
• Plants are grown hydroponically- in nutrient soil solution • Avoids photorespiration
where its contents vary depending on the plants stage of • Dimorphic nature of chloroplasts
growth
• Pests and fungal diseases are fewer, further improving
yield

5.5 C4 Plants
• C3 plants: forms a 3C molecule after splitting the 6C
compound during the light independent stage of
photosynthesis
• C4 plants such as maize, sorghum and other tropical
grasses however, produce a 4C compound first in the
light independent reaction
• Photorespiration: is the reaction when RuBP combines
with oxygen instead of CO2 so Calvin cycle cannot occur
• This usually happens in high temperatures (as stomata
close to prevent water loss, causing O2 build up) and
high light intensity.
• In C4 plants the Calvin cycle occurs in the bundle sheath
o Carbon dioxide is absorbed by mesophyll cells that
5.6 Pigments and the Absorption of Light
contain the enzyme PEP carboxylase which catalyses
the combination of CO2 with PEP (3C) • There are two groups of pigments
o Oxaloacetate (4C) is formed and is converted into o Chlorophylls (Primary Pigments)
malate (4C) o Carotenoids (Accessory Pigments)
o It is then passed onto the bundle sheath cells and CO2 Pigment Colour
is removed forming pyruvate (3C) Chlorophyll 𝛼 Green
o The CO2 continues normally ie the Calvin cycle Chlorophyll 𝛽 Blue
𝛽 carotene Orange
Xanthophyll Yellow

• Absorption spectrum: is the graph above and shows the

absorbance at different wavelengths of light
o A low absorption means that those wavelengths are
not absorbed, but instead are reflected or transmitted
Adaptation ∴ plants seem to be green as it is absorbed least
• Higher optimum temperature than C3 plants (45 oC)
o Carotenoids mainly absorb in the blue-violet region.
• Mesophyll cells tightly packed so not allowing O2 to
• Action spectrum: graph that shows rate of
reach bundle sheath cells
photosynthesis at different wavelengths of light
PAGE 16 OF 44
 CIE A2-LEVEL BIOLOGY//9700
6. INHERITED CHANGE

o Lowest absorbance corresponds to lowest rate of

• A karyogram shows chromosomes that are rearranged
photosynthesis as slower light dependent reactions.
into homologous pairs
• Note that rate is higher at lower wavelengths, this is not
• There are 22 pairs of autosomal homologous
only due to greater absorption but also as lower
chromosomes, wherein one chromosome of each pair is
wavelengths contains more energy
maternal, and the other is paternal
Chromatography
• The 23rd pair is a non-matching sex chromosome
• Grind leaf using a mortar and pestle with solvent such as
• Chromosomes can be distinguished by staining it; each
propanone
pair has distinctive banding patterns
• Leaf extract contains mixture of pigments
• Homologous chromosomes: pair of chromosomes in
• Allow the sample to evaporate to concentrate the
diploid cell that have same structure as each other, with
pigment
the same genes (may not be same allele) at the same
• Draw a pencil line and place extract on it using a capillary
loci, which pair up to form a bivalent
tube
• Locus: position at which a particular gene is found on a
• Place paper vertically in jar of different solvent
particular chromosome
• Solvent rises up paper with each pigment traveling at
• Gene: a length of DNA that codes for a particular protein
different speeds hence pigments separated
• Distance moved by each pigment is unique
• Use Rf value to identify each pigment
𝑑𝑖𝑠𝑡𝑎𝑛𝑐𝑒 𝑡𝑟𝑎𝑣𝑒𝑙𝑙𝑒𝑑 𝑏𝑦 𝑝𝑖𝑔𝑚𝑒𝑛𝑡
𝑅𝑓 =
𝑑𝑖𝑠𝑡𝑎𝑛𝑐𝑒 𝑡𝑟𝑎𝑣𝑒𝑙𝑙𝑒𝑑 𝑏𝑦 𝑠𝑜𝑙𝑣𝑒𝑛𝑡

• Repeat with a different solvent, placing the

chromatogram 90° to the original alignment

PAGE 17 OF 44
 CIE A2-LEVEL BIOLOGY//9700
6.1 Meiosis
• Described as reduction division because chromosomes are halved from diploid (2n) cells to haploid (n)
• Thus, chromosome number is kept constant instead of doubling every generation
• Also causes genetic variation for gametes which leads to natural selection
• In prophase I, homologous chromosomes pair up to form bivalent in a process called synapsis.
• At the end of Telophase II, 4 haploid daughter cells are produced

PAGE 18 OF 44
 CIE A2-LEVEL BIOLOGY//9700
• Variation caused:
o During late prophase 𝐼, crossing over takes place:
homologous chromosomes (bivalents) attach to each
other forming chiasma and switch genetic information
▪ Chiasma: point of contact between two non-sister
chromatids belonging to homologous chromosomes
o During metaphase 𝐼, independent assortment of
genes occurs: pairs of homologous chromosomes lie
independently of each other and randomly at the
equator
o When genetically different gametes fuse at random
6.2 Gametogenesis in Humans
In males:
• Takes place in the tubules of the testes
• Germinal epithelial cells divide by mitosis to produce
diploid spermatogonia which grow to form primary
spermatocytes
• These divide by meiosis 𝐼 to form 2 haploid secondary
spermatocytes which continue with meiosis 𝐼𝐼 forming 4
spermatids that mature into spermatozoa
In females:
• Takes place in the ovaries
• Germinal epithelial cells divide by mitosis to produce
diploid oogonia
• Oogonia start meiosis and become primary oocytes (still
diploid), but meiosis stops at prophase I
• All this occurs before a baby girl is born and at birth has
around 400 000 primary oocytes
• At puberty, primary oocyte continues to finish meiosis I
to produce secondary oocyte and first polar body (small
haploid cell with less cytoplasm; degenerates; gets rid of
half of the chromosomes)
• Each month one secondary oocyte is released into the
oviduct to get fertilised
• If fertilisation occurs, secondary oocyte undergoes
meiosis 𝐼𝐼 to form an ovum and second polar body
• If ovum is fertilised, then a diploid cell is formed called a
zygote → embryo → fetus
o Unequal distribution of cytoplasm: the resulting
zygote receives all of its cytoplasm from the egg, so the
egg needs to have as much cytoplasm as possible.

MALE FEMALE
Produces sperm Produces oocyte
Division of cytoplasm is Division of cytoplasm is
equal unequal
Four gametes produced One gamete produced
No polar bodies Polar bodies
Complete meiosis Incomplete meiosis

PAGE 19 OF 44
 CIE A2-LEVEL BIOLOGY//9700
6.3 Gametogenesis in Plants
In males
• Takes place in the anther
• Diploid pollen mother cells divide by meiosis forming 4
haploid cells.
• The nuclei of these cells divide by mitosis (cytokinesis
does not take place) resulting in cells with two haploid
nuclei
• These cells mature into pollen grains
o One of the nuclei is the tube nucleus and the other is
generative nucleus. The generative nucleus divides by
mitosis to give 2 nuclei, which are the male gametes.
In females
• Takes place in the ovules
• Diploid spore mother cell divides by meiosis to produce
four haploid cells
• All but one degenerates; this cell develops into an
embryo sac
• Embryo sac divides by mitosis 3 times forming 8 haploid
nuclei, of which one becomes the female gamete
• Note: In plants, gametes are not formed directly from
meiosis, instead meiosis is used in producing the pollen
grains and embryo sac which then form gametes by
mitosis
PAGE 20 OF 44
6.4 Genetics
• Alleles are different varieties of the same gene
• Genotype: the genetic composition of an organism
formed by alleles eg the alleles HbA HbS form the
genotype: HbAHbS, HbSHbS, HbAHbA
• A dominant allele is one whose effect on the phenotype
of a heterozygous is identical to one of a homozygote
• A recessive allele is one who does not express itself
when a dominant gene is present
• Codominant alleles have both the phenotypes of each
allele in a heterozygous organism
• A test cross is a genetic cross in which a dominant allele
is crossed with a homozygous recessive organism; the
offspring phenotypes can determine whether the parent
is homo/hetro dominant
• F1 generation is crossing homozygous dominant with
homozygous recessive
• F2 generation is crossing two F1 (heterozygous)
organisms
6.3 Monohybrid Crosses
• A monohybrid cross is a mating between two individuals
with different alleles at one genetic locus of interest
6.4 Multiple Alleles
• More than 2 alleles of a gene, only two of which can
exist in any normal, diploid individual.
6.5 Sex Inheritance
• Y chromosome is much shorter than X and contains
fewer genes
• A person with XX chromosomes is female and XY is male
• Your gender is determined by the father’s sperm as
mother always gives the X chromosome (1:1 chance)
 CIE A2-LEVEL BIOLOGY//9700
6.6 Sex Linkage • A dihybrid cross between two heterozygous species is a
• Sex linkage is the phenotypic expression of an allele that more complicated, as each species will produce 4
is dependent on the gender of the individual and is gametes, giving a ratio of 9:3:3:1
directly tied to the sex chromosomes
• X chromosomes contain a gene that codes for blood
clotting: the factor VIII.
o The recessive allele (h) causes the disease haemophilia
(blood fails to clot)
• This is considered to be a sex linked gene as it is found
on the X chromosome but not found on the Y (thus it is
expressed in males despite being a recessive allele)
• When inherited, females will have 2 copies of this gene
and males would have 1
• Males always express it in their phenotype if it is present
in their genotype (XhY) whereas women require 2
recessive alleles to show expression (homozygous XhXh).
Therefore women can only be effected if both her
mother and father contain the allele.
• Genotypes of sex linked genes are always represented by
symbols that are on the X chromosome e.g. XHXh (carrier)

6.7 Dihybrid Crosses 6.8 Interactions Between Loci

• Deals with the inheritance of two separate genes on
• The effect on phenotypic character by interaction
different chromosomes at once (e.g. eye colour and skin)
between different gene loci; one gene locus could mask
• When cells undergo meiosis to produce gametes, the the phenotypic expression of another.
homologous pairs line up independently of each other
o A/a: alleles of the gene for stem colour.
o D/d: alleles of the gene for leaf shape.

6.9 Autosomal Linkage

• Hence we can predict 4 gamete produced in equal
numbers
• A dihybrid cross between a heterozygous and
homozygous species would give a 1:1:1:1 simple ratio
• Linkage: the presence of two genes on the same
chromosome, so that they are inherited together and do
not assort independently
• Linked gene written in brackets to indicate that they are
on the same chromosome e.g. (EA)(EA) instead of EEAA

• Total linkage is very rare, almost always links are broken

due to crossing over during meiosis
PAGE 21 OF 44
 CIE A2-LEVEL BIOLOGY//9700
6.10 Crossing Over
• Occurs during prophase I where chiasmata formed
between bivalents
• Chiasmata connects with a non-sister chromatid so
maternal and paternal genes are exchanged
• When these exchanged genes form offspring they are
said to be recombinant offspring
5. You must find the degrees of freedom which is =
number of different categories – 1
• If calculated 𝑥 2 is lower than the expected 𝑥 2 in the
table, we accept the null hypothesis, meaning the results
are due to chance and so no significant difference
• And if calculated 𝑥 2 greater or equal to expected 𝑥 2 ,
we reject null hypothesis as difference must be
significant and is not due to chance
• Note: take the probability value of 0.05 as it is the
critical value
Example:
Observed results

• Linkage groups are broken

• Cross over value is calculated by adding the percentage
of offspring that belong to recombinant classes
• This value can be used to measure the distance apart of
the two gene loci
Chance of cross over ∝ distance apart

6.11 Chi-squared (𝒙𝟐 ) Test

• Ratios such as the 9:3:3:1 are only probabilities of Expected results
inheriting the phenotypes
• What we observe may not always be exactly the same as
the expected probabilities.
• Use Chi-squared test: to test whether the difference
between observed and expected results has arisen due
to chance (used for categorical variables eg colour and
• 4 categories, so degree of freedom 4-1 = 3
shape of leaf)
• Using critical value of 0.05, the expected x 2 we should
• Null hypothesis: there is no significant difference
get is 7.82
between observed and expected results
• Our calculated x 2 0.79, which is a probability much
Σ(𝑂 − 𝐸)2
𝑥2 = greater than 0.1
𝐸
Blue colour indicates that this formula will be provided in the exam • As the probability of the difference between expected
1. First work out expected (E) results by using ratio given and observed results is greatly due to chance, we say
𝑝ℎ𝑒𝑛𝑜𝑡𝑦𝑝𝑒 that the difference between them is not significant and
× 𝑛𝑢𝑚𝑏𝑒𝑟 𝑜𝑓 𝑜𝑓𝑓𝑠𝑝𝑟𝑖𝑛𝑔
𝑡𝑜𝑡𝑎𝑙 𝑝ℎ𝑒𝑛𝑜𝑡𝑦𝑝𝑒𝑠 we accept the null hypothesis
2. Then find (𝑂 − 𝐸)2
Note: it is squared to get rid of the negative sign as it is 6.12 Mutation
irrelevant • Mutation: unpredictable change of the nucleotide
3. We then divide each squared number by E and add sequence in DNA
them up to give us 𝑥 2 • Mutagen: substance that increases chances of mutation
4. Now you look up the value in a probability table (ie eg. ionising radiation
probability of any difference between observed and • Two types of mutation:
expected results is due to chance) to see if null o Gene mutation: change in the structure of DNA
hypothesis will be accepted or rejected molecule producing different allele of a gene

PAGE 22 OF 44
 CIE A2-LEVEL BIOLOGY//9700
o Chromosome mutation: changes in structure or o The enzyme tyrosinase is responsible for melanin
number of whole chromosomes in cell production as it is needed in the first two steps.
• Gene mutation can occur in 3 different ways Tyrosinase

Tyrosine DOPA dopaquinone melanin

o Base substitution where simply one base takes
another base’s place o The mutation in the gene coding for tyrosinase results
o Base addition where on/more extra bases are added in its absence or the presence of inactive tyrosinase in
o Base deletion where bases are lost from sequence melanocytes (cells responsible for melanin production)
o Thus, tyrosine can’t be converted to DOPA and so on.
• Base addition and deletion have significant effects on
the structure and function of the polypeptide as it alters
6.15 Huntington’s Disease
the following codons (frame shift).
• A mutation inherited as a dominant allele
• Base substitution may not even have an effect at all
• HD has a variable onset but occurs most commonly in
(silent mutation), as there is more than one codon that
the middle age (30-45)
codes for the same amino acid
• It is a neurological disorder that causes involuntary
• However, all mutations can cause a STOP codon to form,
movements and progressive mental deterioration
causing the polypeptide production to be halted.
• Mutation occurs on chromosome 4 on a gene that codes
6.13 Sickle Cell Anaemia for the protein huntingtin
o Normally, people have small number of triplet CAG
• Example of base substitution
repeats
o Where the 𝛽-globin polypeptide mutates
o The base sequence CTT is replaced by new triplet CAT o With the diseased, the number of CAG repeats is large
(stutter)
o Which changes the 6th amino acid from Glu to Val
• There is an inverse correlation between number of times
• This small difference does not affect the haemoglobin
molecule when combined with oxygen triplet repeats and onset age of condition; eg the more
the repeats, the earlier the onset of the disease.
• But when not combined, the 𝛽-globin molecule becomes
much less soluble and starts to stick to each other
6.16 Gene Control in Prokaryotes
forming long fibres inside red blood cells, pulling the
• Structural genes are genes that code for proteins or
cells out of shape to become sickle shaped
enzymes required by a cell
• They also get stuck in small capillaries, restricting blood
• Regulatory genes are genes that code for proteins that
flow
regulate the expression of other genes
• Repressible enzymes are produced continuously unless
production is repressed by binding a repressor protein to
the operator
• Inducible enzymes are only produced when its substrate
is present. Transcription of the structural gene occurs as
a result of the inducer (the enzyme’s substrate)
interacting with the protein produced by the regulatory
6.14 Albinism gene
• Albinism is when melanin is deficient or completely
missing from irises, skin and hair
• The condition also can be accompanied by poor vision
causing jerky movements of the eye to avoid light
• In classic form: it is an autosomal recessive mutation
wherein individuals must be homozygous for the
recessive allele to show albinism
• Sex linked form: affects the eyes

PAGE 23 OF 44
 CIE A2-LEVEL BIOLOGY//9700
The Lac Operon
• An Operon is a length of DNA containing a cluster of
genes including structural genes and regulatory gene
controlled by a single promoter
• The enzyme 𝛽-galactosidase (inducible enzyme)
hydrolyses lactose to glucose and galactose
• The lac operon consists of promoter, operator and 3
structural genes which are:
o lacZ which codes for 𝛽-galactosidase.
o lacY which allows lactose to enter cell
o lacA which codes for transacetylase
• When no lactose present
o Regulatory gene codes for repressor
o Repressor binds to operator
o RNA polymerase cannot bind to DNA
∴ No transcription occurs
• The repressor protein is allosteric, meaning it has two
binding sites, one for DNA and another for lactose.
• When lactose is present
o Lactose is taken up by bacterium
o And binds to repressor protein, distorting its shape
and preventing it from binding to DNA at operator
o Transcription is no longer inhibited and RNA is
produced
• This mechanism helps avoid waste of energy and
materials by only creating enzymes when required
6.17 Gene Control in Eukaryotes
• Transcription factors: regulate transcription
o Proteins that bind to a specific DNA sequence and
control the flow of information from DNA to RNA by
controlling mRNA formation
• Functions of transcription factors:
o Form part of protein complex that binds with
promoter region
PAGE 24 OF 44
o Activate appropriate genes in sequence allowing
correct pattern for body development
o Responsible for the determination of sex in mammals
o Allows responses to environmental stimuli, such as
switching on correct genes in high temp
o Regulate cell cycle, growth and apoptosis (cell death)
• The plant hormone, gibberellin controls seed
germination by stimulating the increase in transcription
of mRNA coding for amylase
• Gibberellin does this by breaking down DELLA proteins
which inhibit the binding of transcription factor, PIF to a
promoter
• Transcription can then take place resulting in increase of
amylase production
7. SELECTION AND EVOLUTION
Genetic variation is caused by:
• Independent assortment of chromosomes and therefore
alleles
• Crossing over between chromatids of homologous
chromosomes
• Random mating between organisms
• Random fertilisation
• Mutation
7.1 Continuous and Discontinuous Variation
Continuous variation:
• A quantitative difference that has a wide range of
phenotypes
• Intermediate phenotypes are usually what is observed
• Plotting a frequency graph usually gives a bell-shaped
distribution curve
• E.g. Height and weight as these do not have
distinguishable classes but are in a range
 CIE A2-LEVEL BIOLOGY//9700
• Different alleles at a single gene locus have small effects
on the phenotype
• Polygenes genes have an additive effect on a particular
trait
Discontinuous variation:
• A qualitative difference that has clear distinguishable
categories with no intermediates
• It is usually a one to one relation between genotype and
phenotype
• E.g. Blood groups, there is only 4 possible groups
• Different genes have different effect on phenotype
• One or few genes control the characteristic, so alleles on
single gene locus have large effects
Environmental effects on phenotype:
Height for example can be influenced by environmental
factors such as nutrition
Cats can change their fur colour in extremities according
to external temperature eg: dark pigment at low temp
7.2 The t-test
• The t-test is used to assess whether the means of two
normally distributed sets of data are significantly
different from one another
• Similar to the chi-squared test, you always start with a
null hypothesis stating that there is no significant
difference between the two samples
|𝑋1 + 𝑋2 |
t=
𝑠2 𝑠2
√ 1+ 2
𝑛1 𝑛2
o 𝑋1/2is the mean of samples 1 and 2
o 𝑠 21/2 is the standard deviation of samples 1 and 2
o 𝑛1 /2 is the no. of individual measurements in 1 and 2
• Degrees of freedom: total number of samples − 2
• From the probability table we take 0.05 (5% confidence
level) as our critical value
o If probability lower than critical value, null hypothesis
accepted, so difference is due to chance
o If greater or equal, difference is significant and not due
to chance, so reject null hypothesis
PAGE 25 OF 44
7.3 Natural Selection
• Natural selection: the effects of selection pressures on
the frequency of alleles in a population.
• Natural selection raises advantageous allele frequencies
and reduces the disadvantages allele frequencies within
the population
• Natural selection occurs to limit exponential growth of
populations and ensure survival of the fittest.
• Environmental factors that affect population growth:
o Biotic – caused by living organisms e.g. predation,
competition for food, infection etc.
o Abiotic – caused by non-living organisms e.g. water
supply, nutrient levels in soil etc.
• However, due to genetic variation, individuals that are
best adapted are likely to breed and pass on
advantageous alleles to next generations
• Thus, selection pressure causes changes in allele
frequency and gene pool which overtime leads to
evolution.
7.4 Types of Selection Pressures
• Natural selection can act on traits determined by
different alleles of a single gene, or on polygenic traits
• Natural selection on polygenic traits can take the form
of:
• Stabilising selection: when natural selection keeps the
variety of the population the same.
o If wide variation shown, selection pressure acts
against the two extremes.
o Results in a population with a narrower range of the
characteristic
o Tends to keep the variation in a characteristic centred
around the same mean value
 CIE A2-LEVEL BIOLOGY//9700
• Directional selection: when a new environmental factor 7.8 Artificial Selection
or a new allele appears, causing different allele ARTIFICIAL SELECTION NATURAL SELECTION
frequencies to be produced Selection pressure applied Environmental selection
o Selection acts against one extreme, results in change is by humans pressure
in a characteristic in a particular direction Genetic diversity is Genetic diversity remains
lowered high
Inbreeding is common Outbreeding is common
Inbreeding depression Less inbreeding depression
Increased homozygosity Decreased homozygosity
No isolation mechanisms Isolation mechanisms do
operating operate
• Disruptive selection: when conditions favour both Usually faster Usually slower
extremes of a population (this selection maintains Selected feature is for Selected feature is for
different phenotypes) human benefit organism’s benefit
Not for survival/evolution Promotes
survival/evolution
Example of Selective breeding in
• Improving milk yield:
o Individuals showing desired features are chosen to
breed
o Some of the alleles conferring these features are
7.5 Genetic Drift passed on to the offspring
• Genetic drift is a change in allele frequency due to o Again, most desired features are chosen for breeding
chance and is most noticeable in small populations. o This process is continued for many generations
causing the frequency of the desired alleles to increase
• The small sample is unrepresentative of the allele
frequency of the larger population and leads to loss of • Improving crop:
genetic variation. o Introduction of disease resistance as there is a great
loss of yield resulting from infections
• Further genetic drift of the small population leads to
o Incorporation of mutant alleles: These genes code for
further alteration of the allele frequency, leading to
DELLA proteins that reduce the effect of gibberellin
evolution and a new species – Founder’s effect
and produce shorter stems. This allows more energy to
7.6 Hardy-Weinberg Principle be used for producing more seeds/grains instead of
• Used to calculate allele, genotype and phenotype growing tall.
frequencies within a large randomly mating population. o Inbreeding and hybridization:
𝑝+𝑞 = 1 ▪ Inbreeding: mating between two genetically closely
𝑝2 + 2𝑝𝑞 + 𝑞 2 = 1 related species, sharing common ancestry
▪ In breeding depression: Inbreeding plants causes
o 𝑝 represents dominant allele frequency
gene pool to become progressively smaller and
o 𝑞 represents recessive allele frequency
weaker over generations
• Hardy-Weinberg’s principle does not apply when there is
▪ Out breeding produces heterozygous plants that are
o Significant selective pressure against a genotype
healthier and grow taller
o Migration into or out of population
▪ The aim is to get heterozygous and uniformity in
o Non-random mating
genes thus out breeding cannot be used
o Limited population
▪ Therefore, hybrid plants are used instead.
▪ Seeds are taken from companies which inbreed to
produce homozygous plants. These are crossed with
different homozygous varieties to produce different
hybrid offspring.
PAGE 26 OF 44
 CIE A2-LEVEL BIOLOGY//9700
7.9 Theory of Evolution
Charles Darwin forwarded the original theory that natural
selection might be a mechanism by which evolution is
formed by his observation and deductions:
Observation
• Organisms produce more offspring than what is needed
to replace the parents (reproductive potential)
• Natural populations tend to remain stable in size
Deduction
• There is a competition for survival
Observation
• Variation amongst individuals of a given species
Deduction
• The best adapted variants will be selected by natural
conditions, these are the variants that have a selective
advantage and so ‘survival of the fittest’ occurs
This theory was put forward in the past, where they knew
nothing about genes and alleles so now we can improve it
by saying that, natural selection picks particular alleles or
groups of alleles
7.10 Molecular Comparisons
Molecular comparisons allows us to see how similar and
related species are to each other
Comparing amino acid sequence of proteins:
• When amino acid sequence is compared the number of
differences gives a measure of how closely related the
species are
• Differences in primary structure can cause dramatic
change in structure and function however small changes
can leave the overall structure and function same
Example:
Cytochrome C for example was compared between
human, mice and rats
o All three consisted of 104 amino acids
o The sequence of mice and rat cytochrome is identical
o 9 amino acids in human are different from rat/mice
• This comparison suggests that mice and rats shared a
recent common ancestor, but not with humans
Comparing amino acid sequence of mitochondrial DNA:
• Difference in mtDNA can be used to study the origin and
spread of species
• mtDNA is inherited through the mother only
• mtDNA is circular and not protected by histone proteins,
so they cannot undergo crossing over hence the only
possible way of change is through mutation
• mtDNA mutates at around one mutation in 25000 years
PAGE 27 OF 44
• This has provided us with evidence that the origin of
H.sapiens was from Africa around 200 000 years ago
7.11 Speciation
• Speciation is the evolutionary process by which new
biological species arise
• The main feature biologists use to decide whether two
organisms belong to different species is their inability to
interbreed successfully (reproductive isolation)
• Reproductive isolation can take different forms:
Prezygotic
o Individuals don’t recognise each other as mates or
don’t respond to mating behaviour
o Physically being unable to mate
o Inability to fuse male and female gametes
o Incompatibility of pollen and stigma in plants
Postzygotic
o Failure of cell division in the zygote
o Non-viable offspring (dies soon)
o Viable but sterile offspring
Allopatric speciation: when speciation occurs where two
populations are separated from each other geographically
o Mixing of the two is prevented, and each have
different selection pressures acting on the populations
o This results in different alleles being selected for, and
soon the morphological, physiological and behavioural
features become so different that the two populations
can no longer interbreed even if the barrier is removed
Sympatric speciation: is when a new species is evolved
from a species that inhabits the same geographic region
o The most common way in which sympatric speciation
occurs is by polyploidy
▪ A polyploidy is an organism with more than two
complete sets of chromosomes in its cell
▪ This can happen if meiosis is abnormal during gamete
formation, resulting in a gamete with 2 sets of
chromosomes (diploid)
o If two diploid gametes fuse, it results in 4 complete
sets of chromosomes - tetraploid zygote
o If a diploid gamete joins with a haploid gamete they
form a triploid zygote
o Polyploidys are often sterile as they can’t divide during
meiosis. This is because all the sets try to pair up at
once and end up in a muddle.
 CIE A2-LEVEL BIOLOGY//9700
o However, they can grow perfectly well & reproduce
asexually
o For example, a tetraploid organism from a diploid
parent cannot interbreed successfully and become
different species.
▪ Autopolyploid: polyploidys that are derived from a
single species and are infertile.
o Allopolyploid: polyploidys that are derived from
different species. Note that meiosis happens more
easily here as the sets of chromosomes are from
different species and can pair up. They are fertile, but
cannot breed with parent species (self-fertile).
7.12 Extinction
• Living organisms are dependent on the environment and
other species for their survival. When the environment
changes, organisms that cannot adapt become extinct
• There are many factors that can cause extinction:
competition for food and resources, climate change,
habitat loss, hunting, diseases, etc
8. HOMEOSTASIS
Homeostasis is maintaining a relatively constant
environment for the cells within the body, despite
changes in external environment
• Controlled by the composition of blood, and hence the
tissue fluid
• Features of tissue fluid influences cell activity in many
ways, such as:
o Temperature- low temp, slow metabolic reactions.
High temp however denatures enzymes and proteins
o Water potential- low water potential would cause
water to move out of cells which slows/stops cell
PAGE 28 OF 44
functions. High water potential however causes cells to
swell and may burst
o Conc. of glucose- too less, no energy for cell to respire,
too high would affect osmotic balance and disturb cells
8.1 Homeostatic Control
• Involves receptor that detects stimuli
o A stimuli is a change in physiological factors, such as
temperature, pH of blood, water potential etc
• Receptor sends information to the central control in the
brain or the spinal cord
• The input is processed and instructions are sent to the
effector
o Effectors such as muscles and glands cause the factor
to return to its ideal value or set point
• This is done through two coordination systems:
o Nervous system, electrical impulse along neurons
o Endocrine system, in the form of chemical messengers
(Hormones) that travel in the blood
Negative feedback
• Negative feedback keeps factors within narrow limits,
making it close to set point as possible
• When a factor is increased, an effector is stimulated that
makes the factor decrease, and vice versa
Positive feedback
• Is not used in keeping conditions constant as it increases
effect when stimulus is increased
• This is useful in other areas such as transmission of
nerve impulses where the factor must be increased
8.2 Thermoregulation
• Involves maintaining a constant core body temperature
by both the nervous and endocrine systems
• The hypothalamus is the central control for body
temperature, consisting of thermoreceptor cells that
monitor the temperature of the blood and keep it close
to set point.
• The skin also contains receptors that sense the change in
temperature of the surroundings giving the
hypothalamus an early warning
Decrease in temperature
• Vasoconstriction- contraction of arteriole walls that
supply blood to capillaries near skin, restricting blood
flow and preventing heat loss, shunt vessels opened
• Shivering- involuntary contraction of skeletal muscle,
generating heat for blood to absorb
 CIE A2-LEVEL BIOLOGY//9700
• Raising body hairs- traps air (good insulator)
• Decreasing production of sweat- reduces heat loss by
evaporation from skin surface
• Secretion of adrenaline & Thyroid stimulating hormone
(TSH)- causes increase in metabolic rate and heat
production especially in the liver
Increase in temperature
• Vasodilation- arteriole wall relaxes, allowing more blood
flow and increase loss of heat to surroundings
• Lowering body hairs- less air trapped, less insulation,
and more heat lost
• Increasing sweat production- sweat produced causes
more energetic molecules to escape and carry heat away
8.3 Excretion
Deamination is the removal of an amino group (NH2) from
a molecule. This is done in the liver when there is an
excess of protein, rather than wasting a useful energy
source
• The –NH2 and a hydrogen atom are removed leaving
behind a keto acid
Urea formation
• Since ammonia is very soluble and highly toxic
compound it is converted immediately to urea
2NH3 + CO2 → CO(NH2)2+ H2O
• Urea is the main nitrogenous excretory product,
however we also produce creatinine and uric acid
• Creatine is made in the liver from amino acids that is
used as an energy store in muscles
• Uric acid is made from the breakdown of purines
8.4 Structure of the Kidney
• In the cortex:
o Bowman’s capsule
o Proximal convoluted tubule
o Distal convoluted tubule
PAGE 29 OF 44
• In the medulla:
o Collecting duct
o Loop of Henle
8.5 Ultrafiltration
• Involves filtering small molecules out of the glomerulus
and into the Bowman’s capsule due to hydrostatic
pressure build up
• How it happens:
o Hydrostatic pressure builds up in the glomerulus due
to the wider afferent and narrower efferent arterioles
o This causes the hydrostatic blood pressure in the
glomerulus to rise above that of the Bowman’s
capsule.
o Water from blood therefore goes down its water
potential gradient through the endothelium of the
capillary walls, the basement membrane and
podocytes, thus filtering substances.
▪ Endothelium: one cell thick cell with many holes
▪ Basement Membrane: makes up inner lining of
bowman’s capsule and acts as filter for large
molecules eg large Mr proteins, WBC and RBC
▪ Podocytes: inner lining of bowman’s capsule with
large holes
8.6 Reabsorption in Proximal Convoluted
Tubule (PCT)
• The glomerular filtrate is almost identical to the plasma’s
composition except it has no plasma proteins
• Many of the substances however are needed to be kept
in the body, thus most reabsorption occurs in the PCT
• Adaptation of cuboidal epithelial cells:
o Microvilli to increase surface area for many co-
transporters for maximum reabsorption
o Tight junction between cells so that fluid can’t pass
between them
o Many mitochondria to provide ATP for (Na+–K+) pump
on basal membrane
 CIE A2-LEVEL BIOLOGY//9700
o Folded basal membrane providing large surface area
for (Na+–K+) pump
1) Removal of Na+ from the cell: Na+–K+ pumps in the
basal membrane use ATP pumping 3 Na+ out and 2K+ in,
lowering its concentration inside the cell
2) Passive movement of Na+/glucose/amino acid inside
the cell:
o Na+ goes down its concentration gradient via a
cotransporter that brings along glucose/amino acids.
o This a secondary active transport as ATP was not used
for pumping Na+ into the PCT cell but has occurred as a
result of actively transporting Na+ out of the cell
o Glucose and amino acids diffuse down their gradient
from cell into blood via transport proteins in the basal
membrane
3) Reabsorption of water:
o Removal of ions from the tubule increases its water
potential, and increases the solute potential of the cell
o Thus, water diffuses down its gradient into the cell,
and is reabsorbed in the blood via osmosis
4) Reabsorption of urea: urea is a small molecule and
passively gets reabsorbed
8.7 Reabsorption in Loop of Henle
1. Na+ & Cl- are actively transported out of higher end of
ascending limb into the tissue fluid
2. This increases concentration of ions in tissue fluid
PAGE 30 OF 44
3. Water is therefore lost from the descending limb
4. Loss of water concentrates Na+ and Cl− along the
descending limb.
5. This concentrates the fluid inside the loop, so ions
passively move down their concentration gradient, into
the tissue fluid
Distal Convoluted Tubule (DCT)
• First part functions the same way as ascending limb
• Second part functions the same way as collecting duct
Reabsorption of water in DCT and Collecting duct
• Fluid in ascending limb is dilute due to loss of ions and
urea, concentrating tissue fluid in medulla
• When fluid enters collecting duct from DCT, it returns to
the concentrated medulla region, thus water moves out
by osmosis into the tissue fluid and is reabsorbed,
concentrating urine
8.8 Osmoregulation
• Involves the control of water potential in body fluid
• Osmoreceptors in the hypothalamus constantly monitor
water potential in the blood
Decrease in blood water level
1. Osmoreceptors detect and send impulses to the
posterior pituitary gland to secrete antidiuretic
hormone (ADH)
2. ADH in the blood binds to receptors on the cells of
collecting duct, activating intracellular enzymes
3. Vesicles that contain aquaporin in the cell are
stimulated to fuse to membrane
4. This causes duct to become permeable to water hence
water moves out, down its conc. gradient
• Note: volume of urine decreases and becomes more
conc.
Increase in blood water level
• Osmoreceptors no longer stimulate ADH production, so
aquaporins moved back into cytoplasm as vesicles,
making cells impermeable to water again
• This process is very slow because ADH molecules take
15-20 mins to be broken down in the blood and another
15-20 mins for aquaporins to be removed from the
membrane
8.9 Control of Blood Glucose
• When glucose is in low concentration our cells may not
have enough glucose for respiration, hence might not be
able to carry out its normal function
 CIE A2-LEVEL BIOLOGY//9700
• On the contrary, high concentrations can effect normal
behaviour of cells as they may lose water due to the
concentration gradient built (cells become flaccid)
• The homeostatic control is carried out in the pancreas by
a tissue called the islets of Langerhans which consisting
two types of cells:
o 𝛼 cells which secrete glucagon
o 𝛽 cells which secrete insulin
• After a meal containing carbohydrates, glucose is
digested and passed into the blood
• When Blood glucose levels rise
• The 𝛼 and 𝛽 cells detect the change
o 𝛼 responds by stopping secretion of glucagon
o 𝛽 responds by secreting insulin into the blood
• Insulin is a signalling molecule that targets the liver and
muscle cells and binds to a receptor
• This stimulates the cells to increase rate of glucose
absorption by making vesicles carrying glucose
transporter proteins (GLUT) to bind onto cell membrane
• Glycogenesis occurs which is the condensing of glucose
molecules to glycogen which can later be converted to
glucose in respiration.
• Glucokinase enzyme also stimulated which
phosphorylates glucose, trapping it inside (as it can’t
pass out through the GLUT)
• When blood glucose levels fall (or adrenaline level rise)
o 𝛼 responds by secreting glucagon into the blood
o 𝛽 responds by stopping secretion of insulin
• Glucagon binds on to its receptor on liver cells that
activates the G protein
• G protein activates a membrane enzyme that catalyses
conversion of ATP to cyclic AMP
• Cyclic AMP binds to kinase enzymes that activates other
enzyme cascade reactions which finally catalyse the
breakdown of glycogen to form glucose
• Gluconeogenesis: new glucose made from amino acid
and lipid
PAGE 31 OF 44
• Note: muscle cells don’t have glucagon receptors
8.10 Diabetes
• Insulin dependent diabetes, Type 1: pancreas is
incapable of secreting enough insulin due to:
o Lack of gene that codes for insulin
o Autoimmune disease
o Solution: insulin injections and mini pumps, controlled
diet
• Non-insulin dependent diabetes, Type 2: pancreas
secretes insulin but liver and muscle cells do not respond
properly.
o Hunger and thirst are a consequence as kidney cannot
reabsorb glucose, which passes in urine along with
extra water and salts
o Instead cells metabolise fats and proteins instead
which leads to build up of keto acid which is toxic.
o Note: blood glucose levels may fall as there was no
glycogen stored when glucose was in the blood.
8.11 Urine Analysis
• Much easier to collect than blood samples
• Urine tests can give early indications of health problems
o Diabetes: presence of excessive glucose and ketones
in urine, as blood glucose level rises above renal
threshold and so not all reabsorbed
o High blood pressure/kidney infection: presence of
proteins as they are too large to be filtered out
8.12 Dipsticks and Biosensors
Dipsticks
• Urine analysis to measure: pH,
glucose, ketones and proteins
• Glucose dipsticks contain glucose
oxidase and peroxidase
 CIE A2-LEVEL BIOLOGY//9700
• Positive test: glucose oxidase oxidises glucose to form • Influx of K+ ions inside the cell increases the solute
gluconolactone and hydrogen peroxide potential and reduces water potential, thus water enters
o Peroxidase catalyses reaction of hydrogen peroxide by osmosis making cells turgid
and chromogen (colourless chemical) forming a brown • The stomata has uneven cell wall thickening; walls
compound adjacent to pore is very thick, whereas the walls furthest
• The colour formed is compared to a chart, the more from pore is thin
glucose present, the darker the colour (semi- • When cells are turgid, the outer end cells lengthen,
quantitative) causing the guard cells open.
Biosensors
Allow people with diabetes to monitor their
blood glucose concentration much quicker
than dipsticks
• They also contain glucose oxidase which
catalyses the same reaction
• Stomata closes when hydrogen ion pumps stop and
• However, a current is generated, detected
potassium ions leave the guard cells
and amplified which gives a reading within
• Water then leaves the cells, causing it to become flaccid
seconds (quantitative)
and closing the stomata
• The more the glucose present the greater the reading
Abscisic acid and stomatal closure
8.13 Homeostasis in Plants • A stress hormone that causes the closure of stomata in
difficult conditions
• Stomata has daily rhythms of opening and closing even if
• ABA binds to receptors that inhibit proton pumps and
kept in constant light/dark
stimulate movement of Ca2+ ions into the cell.
• Opening during day maintains inward diffusion of CO2
• Ca2+ acts as a second messenger, activating channel
and outward diffusion of O2 and water vapour
proteins to allow negatively charged ions to move out
• Closing during the night as it does not respire and
• This causes potassium ions to move out and also closes
conserves water
K+ channels so that they can’t enter
• Stomata open when:
• Water potential increases inside the cells, which diffuses
o Increase in light intensity
down its water potential gradient by osmosis.
o Low CO2 concentrations
• The cell becomes flaccid and stomata closes.
• Stomata close in:
o Darkness 9. COORDINATION
o High CO2 concentrations
o Low humidity 9.1 Types of Information Transfer
o High temperature NERVOUS ENDOCRINE
o Water stress SYSTEM SYSTEM
FORM OF Electrical Chemical
8.14 Opening and closing of stomata TRANSMISSION impulses messengers
Opening of stomata (Hormones)
FORMED AT Sensory neurone Secretory gland
• ATP proton pumps actively move H+ ions out
generates
of the guard cells
impulse
• This causes potassium channels to open & TRAVEL IN Neurones Blood
move into the cell due to the (endocrine)
electrochemical gradient produced SPEED Instantaneous Slow
o Electrochemical gradient is the combination of an DURATION Short-term Long lasting
electrical gradient caused by the release of H+ ions EFFECTS Localised Widespread
(making inside more negative) and a concentration
gradient due to low levels of K+ inside
PAGE 32 OF 44
 CIE A2-LEVEL BIOLOGY//9700
RECEPTOR On cell surface Cell surface • The effector acts before the brain processes the impulse
LOCATION membrane membrane OR and produces any voluntary movement.
within cell • Hence, this is a reflex reaction, which is fast, automatic
ENERGY Large amount Less required and is useful in response to danger
• Both involve cell signalling
• Both involve signal molecule binding to receptor
• Both involve chemicals

9.2 Neurones
3 different types of neurones:
• Sensory neurone: Transmits impulses from receptor to
CNS
o Swelling of spinal cord containing cell body known as
ganglion
9.4 Myelin
• Myelin is made when specialised cells called Schwann
Cells which wrap themselves around the axon, enclosing
it within many layers
• The uncovered regions between Schwann cells are called
Nodes of Ranvier
• About a third of axons on motor and sensory neurons
are surrounded by myelin sheaths

• Intermediate Neurone (Relay/Connector): transmit

impulse from sensory to motor neurone
o Found entirely in CNS
• Motor Neurone: Transmit impulses from CNS to effector
o Cell body lies within CNS and contains the nucleus
o Dark specks in cytoplasm are rough ER regions
Speed of Conduction
• Myelination stops depolarisation from occurring, greatly
increasing the speed of conduction
• It also prevents the leakage of ions and increases
insulation, increasing speed of conduction.
• Myelin also causes saltatory conduction which is when
action potentials jump from one node to the next, which
is about 50 times faster than unmyelinated axon
• Diameter also affects speed of transmission; with
thinner axons, there is greater resistance, hence,
transmission is slower

9.5 Transmission of Nerve Impulses

9.3 Reflex Arc
A reflex arc is the pathway along which impulses are
transmitted from receptor to an effector without involving
the ‘conscious’ regions of brain
• Impulses travel from sensory to relay (not always) and
finally to motor neurone
Nerve impulses are signals transmitted along the axon,
consisting of waves of depolarisation, causing changes in
the potential difference across the membrane (action
potential)

PAGE 33 OF 44
 CIE A2-LEVEL BIOLOGY//9700
Resting potential
Resting axons have a slightly negative electrical potential
inside, producing a potential difference of about -70m𝑽
inside compared to the outside
• Achieved by:
o Plasma membrane being impermeable to Na+ /K+
o Sodium-potassium pumps that actively pump 3 Na+
out and 2K+ in, increasing the concentration of K+
inside, and Na+ outside
o There are more K+ channels than there are Na+,
therefore K+ diffuses down its concentration gradient
(outside the cell) faster than Na+ diffuses in.
o Many large negatively charged molecules inside cell
Action Potential
It is the change in potential difference across the
membrane due to changes in permeability of the
membrane to Na+/K+ ions
• An initial stimulus causes the opening of some voltage-
gated channels causing Na+ to rush in, down its
electrochemical gradient
• This causes the potential difference across the
membrane to become less negative and is called
depolarisation.
PAGE 34 OF 44
• If this potential difference reaches -50m𝑉, then many
more channels open, causing inside to become +30m𝑉
o This wave of depolarisation is an example of positive
feedback
• Hence for an action potential to be produced, the
potential must be raised to a minimum threshold
potential of -50m𝑉
o If lower than this, an action potential will not be
generated
o This is known as the all-or-nothing law as the neurones
either transmit impulse or do not
• After 1ms, all Na+ voltage-gated channels close & K+
gated channels open, causing K+ to diffuse out, thus
repolarising the membrane.
• The sodium potassium pump continues pumping these
ions and maintaining their concentration across the
membrane, allowing more action potentials to occur.
• Local circuits are set up, where the permeability of the
neighbouring region of the axon is increased
• Axons have a refractory period after the action
potential, where it is unresponsive to new stimulations.
Its consequences are:
o Action potentials do not merge and so are discrete
o There is a minimum time between action potentials
occurring at one place on neurone
o Length of refractory period determines max frequency
at which impulses are transmitted
o Hyper polarisation occurs when the cell potential
becomes more negative than resting potential as there
is an excess outflow of K+
 CIE A2-LEVEL BIOLOGY//9700
How action potentials carry information
• Action potentials do not change in size whether large or
small stimulus & has constant peak value of +30m𝑉
• The brain receives action potential from specific position
of neurones and interprets the nature of the stimulus eg
position: retina, nature: light
Strength of stimulus
o The brain interprets this from the frequency of the
action potential-stronger stimuli have larger frequency
o Also strong stimuli cause more neurones to be
stimulated hence the number of neurones carrying
action potential can tell us about the strength
9.6 Receptors
• A receptor cell responds to stimulus by converting
energy from one form to electrical impulse, initiating an
action potential (acts as a transducer)
• Receptor cells are often found in sense organs and are
specialised cells which detect specific type of stimulus
• Some receptors are the ends of sensory neurones, thus
there is no synapse between the receptor cells and
sensory neurones.
Tongue
• The tongue is covered in many papillae, each papilla has
many taste buds over its surface and within each taste
bud lies around 50-100 chemoreceptors that detect
different chemicals, giving different sensations
• Eg: sodium chloride (salt) as stimulus
• Na+ ions diffuse through highly selective channels of
microvilli and cause depolarisation of the membrane:
receptor potential.
• If sufficient stimulation is produced, voltage-gated Ca2+
channels open; Ca2+ then enters, causing exocytosis of
neurotransmitter vesicles
• Neurotransmitters cause action potential in the sensory
neurone and eventually reaches the cortex of the brain
• Note: if receptor potential is below the threshold, it
causes a local depolarisation of the receptor cell and
doesn’t stimulate the sensory neurone to send impulses.
9.7 Synapses
• Region where two synapses meet, there is a small gap
called the synaptic cleft
Cholinergic synapse
• Synapses that have acetylcholine (ACh)
PAGE 35 OF 44
o Action potential stimulates the opening of voltage
gated Ca2+ channels at the presynaptic knob, causing
an influx of Ca2+ into the cytoplasm
o This causes exocytosis of ACh vesicles, which fuse with
the pre synaptic membrane, then diffuse across the
synaptic cleft
o ACh has a complementary shape to the chemically
gated receptor protein on the post synaptic
membrane, and binds to it
o This changes the shape of the protein and opens the
channel for the entry of Na+
o Na+ depolarises that part of the membrane; if pd is
above threshold, an action potential is generated
o Acetylcholinesterase recycles Ach by breaking it into
acetate and choline, preventing the permanent
depolarisation of the membrane.
o Choline returns to presynaptic neurone and combines
with Acetyl coA to form Ach again.
Role of synapses:
1. Ensures one-way transmission as the receptors are
only in post synaptic neurone and vesicles are only in
presynaptic neurone
2. Decreases the overload of information in the brain as
impulses with low frequencies do not reach the brain
3. Involved in memory and learning due to the formation
of new synapses that links neurones involved
4. Interconnection of nerve pathways: sensory and relay
have many dendrite increasing surface area for many
synapses. This connects neurones from different parts
of the body and spreads information throughout.
 CIE A2-LEVEL BIOLOGY//9700
9.8 Structure of striated muscle
• Striated muscle is multinucleate (syncytium) and
consists of several tissues eg connective, nerve, striated
muscle, blood.
• It is made up of bundles of muscle fibres/cells (fascicles)
• Each muscle fibre is made up of regular arrangement of
myofibrils, which produce the striated appearance of
muscle fibres
Structure of muscle fibre
• The sarcolemma (cell membrane) splits into many
infoldings called T-tubules
• Sacroplasm (cytoplasm) contains many mitochondria
that generate ATP for muscle contraction
• The sarcoplasmic reticulum (SR) (endoplasmic
reticulum) have many protein pumps that transport Ca2+
into the cisternae of SR
9.9 Structure of the Myofibrils
• Myofibrils are made of contractile units called
sacromeres (between two Z discs) which are made of
thin and thick protein filaments
• Myosin: fibrous protein with globular head that makes
up thick filament
PAGE 36 OF 44
• Actin: globular protein; two chains of actin overlap to
make up thin filament
• Tropomyosin: fibrous protein twisted around actin chain
• Troponin: protein that is attached to the actin chain at
regular intervals
• Z line: where actin filaments are attached to
• M line: where myosin filaments are attached to
• A band: includes the darker parts in the centre where
actin and myosin overlap
• H band: the grey area within the A band where only
myosin is present
• I band: the white area next to the Z line where only actin
is present
9.10 How muscles contract
• Muscles movement is caused by contraction, causing Z
discs to pull closer together by a process of sliding
• The energy comes from the ATP in myosin heads (an
ATPase)
Process from stimulation
o Sarcolemma is depolarised by an incoming action
potential which spreads along membrane and down
the T-tubule
o Calcium ions are released from sarcoplasmic reticulum
(using ATP) and bind to troponin, causing it to change
shape
o This in turn causes tropomyosin to move, exposing
myosin binding sites on actin filament
o Myosin heads bind with this site forming cross-bridges
o Myosin heads tilt, pulling actin filaments towards
centre of sarcomere (M line)
 CIE A2-LEVEL BIOLOGY//9700
o The heads hydrolyse ATP, providing energy for heads
to let go of actin and return to original position so that
it can bind again to exposed site
o This process continues as long as binding sites are
open and ATP is in excess
o It can be reversed by relaxation of muscle (no cross
bridge) and contraction of antagonist muscle that pulls
filaments further away, lengthening sarcomere

• During contraction, the A band is unaffected however

both H and I bands decrease in length
Providing for muscle contraction
• ATP can be provided from little ATP found in muscle by
respiration and lactic fermentation
• Creatine phosphate stores is an immediate source of
energy that regenerates ATP in the absence of
respiration
creatine phosphate + ADP → creatine + ATP
• When demand for energy has reduced, creatine is
recharged to form creatine phosphate in the presence of
ATP from respiration
• When there is an energy demand and not enough ATP to
regenerate creatine phosphate, creatine is converted to
creatinine and excreted
9.11 Hormonal Communication
• Hormones are made in endocrine glands (ductless) and
are secreted into the blood
Hormonal control in menstrual cycle
• The menstrual cycle is coordinated by the anterior
pituitary gland and by the ovaries
• The anterior pituitary gland secretes Follicle Stimulating
Hormone (FSH) and Luteinising Hormone (LH)
• The corpus luteum (follicle after releasing gamete)
secretes both oestrogen (stimulates endometrium to
grow, thicken and develop numerous blood capillaries)
and progesterone (to maintain endometrium)
PAGE 37 OF 44
• FSH and LH are in relatively high concentrations during
menstruation (4-8 days) and so cause one follicle to
mature
• The presence of FSH and LH stimulates oestrogen to be
produced by the cells surrounding the follicle
• Oestrogen however, has a negative feedback on FSH and
LH so their concentrations decrease
• When oestrogen reaches a level 2-4 times initial value, it
stimulates a surge of LH, causing the ovarian follicle to
burst and ovulation occurs (14-36 hours after the surge)
• The corpus luteum is now formed, releasing
progesterone and some oestrogen
• Progesterone inhibits secretion of FSH and LH so that no
more follicles develop
• Corpus luteum begins to degenerate, decreasing
progesterone and causing menstruation
Birth Control
• Birth control pills can contain progesterone only or both
progesterone and oestrogen (combined)
• The progesterone pill may not prevent ovulation to
occur but they reduce the ability of sperm to reach the
egg cell by increasing mucus levels in the cervix
• The combined pill supresses secretion of FSH and LH due
to the negative feedback from high levels of
progesterone and oestrogen
 CIE A2-LEVEL BIOLOGY//9700
• During the 7 days of menstruation pills are not taken to Adaptations to avoid energy waste
drop progesterone levels and cause menstruation, • Stimulation of single hair doesn’t trigger closure eg rain
reassuring that woman is not pregnant or debris
• Note: pills must be taken daily to be effective as missing • Gaps between stiff hairs allow tiny insects to crawl out,
a single day could cause ovulation so plant doesn’t waste energy to consume small meals

9.12 Electrical Communication in Plants 9.13 Chemical Communication in Plants

Venus fly trap: • Two types of plant growth regulators
• A carnivorous plant that obtains nitrogen compounds by o Auxins: influence elongation of roots and shoots
digesting small animals o Gibberellins: seed germination and stem internode
elongation
• They travel directly from cell to cell (diffusion/active
transport) or carried in xylem/phloem sap
Auxins
• Plants make several chemicals known as auxins, of which
the main one is IAA
• Auxins are synthesised in growing tips/meristems
• Auxins bind to a protein receptor which stimulates
ATPase to pump in H+ into cell walls, reducing its pH.
• Proteins called expansins are activated at low pH,
loosening cellulose microfibril linkages
• Water is absorbed by osmosis and pressure potential
causes the wall to stretch, elongating the cell
• Nectar secreting glands attract insects
• Auxins also inhibit lateral growth so that plant grows
• Each lobe has three sensory/ trigger hairs that respond
taller
when deflected
Gibberellins and stem elongation
• Outer edges have stiff hairs that interlock to trap insect
• The dominant allele 𝐿𝑒 causes the synthesis of the last
• Surface of lobes has glands that secrete digestive
enzyme that produces active form of gibberellin, GA1
enzymes
• Active gibberellin stimulates cell division and cell
Action of shutting the trap
elongation whilst interacting with auxin, causing the
• The deflection of a sensory hair opens Ca2+ channels at
plant to grow tall
cells at the base of hair, causing inflow of Ca2+ and
• Plants that are homozygous and have the recessive allele
generating receptor potential (depolarisation)
𝑙𝑒 produce a non-functional enzyme (due to substitution
• If two hairs (or one hair touched twice) are stimulated
mutation in its primary structure)
within 20-35s, action potentials travel across the lobe to
• Thus, active gibberellin is not produced and so the plant
close it.
is genetically dwarf
o H+ ions are pumped into the cell walls, breaking cross
• Applying active gibberellin to plants that would remain
links (acid growth hypothesis)
short can stimulate them to grow tall
o Calcium pectate ‘glue’ in middle lamella dissolves
Gibberellins and seed germination
o Ca2+ enters the hinge cells causing water to enter by
• Seeds are in a state of dormancy; this allows it to survive
osmosis hence expanding the hinge cells
through cold winters and is only activated when enough
o Lobes of the leaves flip from convex to concave rapidly
water is present
(change in elastic tension)
• Further deflection of hairs stimulate entry of Ca2+ into
gland cells, causing exocytosis of vesicles containing
digestive enzymes.
• Mechanical energy converted to electrical energy
PAGE 38 OF 44
 CIE A2-LEVEL BIOLOGY//9700
10. GENETIC TECHNOLOGY
Genetic engineering: the transfer of genes from one
organism into another (of the same/different species) to
express the gene into its new host.
Recombinant DNA (rDNA): is DNA made by joining lengths
of nucleotide from two or more different sources
• Steps essential for producing genetically modified
organism:
o Identify gene and either:
▪ Cut/ splice from chromosome
▪ Synthesise from reverse transcription of mRNA
▪ Synthesise from free nucleotides
o Make multiple copies by polymerase chain reaction
(PCR)
o Insert gene into vector:
▪ Plasmids
▪ Viruses
▪ Liposomes- tiny spherical sacs made of phospholipid
molecules
o Insert vector with new gene into the cell
o Cells with the new gene are identified and cloned
10.1 Identifying the Gene
Cut from chromosome:
• Restriction Endonuclease: enzyme that comes from
bacteria which can breakdown DNA of invading virus
(bacteriophages).
o ‘Endonucleases’ as they cut the DNA from the sugar
phosphate backbone
o These enzymes bind to specific target site on the DNA
molecule which has a specific base sequence
o Usually they bind to (inverted) palindromic sites, sites
in which the sequence reads the same in
complementary strands when read from 5’ to 3’
PAGE 39 OF 44
o Can form either:
▪ Blunt ends: straight cut across sugar phosphate
▪ Sticky ends: short unpaired, staggered ends that
can easily form H bonds with complementary bases
cut using same restriction enzyme.
Using reverse transcriptase
• By using the reverse transcriptase enzyme, free
nucleotides, mRNA and DNA polymerase, we could
obtain a cDNA strand (complementary DNA)
• This process, however requires you to find the mRNA
molecules in a cell cytoplasm
Synthesising from nucleotides:
• Since proteins have now been sequenced, we can
synthesise DNA artificially from nucleotides.
• The sequence of nucleotides is held in a computer that
directs the synthesis of short fragments of DNA (ref
section 10.7 Bioinformatics). The fragments are then
joined to make longer nucleotides that can be inserted
into plasmids.
10.2 Inserting Gene into Vector
Plasmids: small, circular, double-stranded DNA that is
used as a type of vector, which transfers new genes into a
recipient cell
• To obtain plasmids, bacteria are treated with enzymes to
break their cell walls and are then centrifuged to
separate chromosomes from plasmids.
• Plasmid is then cut open using same restriction enzyme
used for the DNA so that sticky ends are complimentary
• Plasmid and DNA are mixed together
• DNA ligase then links sugar phosphate backbone of DNA
with plasmid, forming rDNA.
Properties of plasmids allowing them to be used as
vector:
• Low molecular mass: can be taken up by bacteria easily
• Polylinker: a short length of DNA containing several
target sites for different restriction enzymes
• One or more marker genes can be added, allowing cells
that take up recombinant plasmid to be identified,
making it easy to screen
 CIE A2-LEVEL BIOLOGY//9700
• An origin of replication so that they can be copied • Movement of charged particle in response to electric
• Resistant to shearing field depends on:
• Easy to isolate in large quantities o Net charge: +ve molecules move towards anode (+),
-ve molecules move towards cathode (-); highly
10.21 Inserting and identifying bacteria with charged molecules move faster.
rDNA o Size: smaller molecules move faster
• Bacteria are put into solution with high Ca2+ conc, are
cooled and then given electric shock to increase chances
10.31 Electrophoresis of Proteins
of plasmid passing through cell membrane • Proteins are made up of amino acids and the charges on
• Only about 1% take up the plasmid and are said to be these amino acids depend on R groups present and pH
transformed
• In the past, we used to use agar plates containing an
antibiotic to identify the bacterium with the plasmid, but
this causes unnecessary resistant strains to be formed
• Other genetic markers:
• In acidic pH, NH2 R groups (bases) gain a proton and
o A gene from jellyfish codes for an enzyme that
become NH3+, hence net charge becomes positive ∴
produces GFP (green fluorescent protein) needs to be
moves towards cathode
inserted into the rDNA (with its promoter), which
• In basic pH, the COOH R groups (acids) lose their protons
fluoresces in UV light.
and become COO–, hence net charge becomes negative
o If an organism contains GUS assay enzyme and is
∴ moves towards anode
incubated with some specific colourless/non-florescent
• In neutral conditions, the NH3+ is cancelled by the COO–
substrates, it can transform them into coloured or
so it depends solely on the R group
fluorescent substances.
• E.g. haemoglobin in sickle cells contains slightly lower
o These are easier methods to identify bacteria and also
negative charge than normal as it’s R group is non-polar
more economical than using antibiotic resistance genes
(valine) hence when separated sickle cell moves less
Promoters: controls the expression of genes
than that of normal (non-polar valine replaces polar
• Region of DNA to which RNA polymerase binds as it
starts transcription of the template strand. glutamic acid)
• Promoters only allow synthesis of genes that are
10.32 Electrophoresis of DNA
required & so waste less energy on unwanted proteins
• Fragments of DNA move towards the anode as it has
o Eg B-galactosidase is made only when the bacteria is
negatively charged phosphate groups
growing in a medium containing lactose, in the absence
• Genetic profiling (fingerprinting): sequencing a length of
of glucose.
DNA of one organism and comparing it to another by
• In order for gene inserted into bacteria to be expressed,
looking at the ‘variable number tandem repeats’ (VNTRs)
appropriate promoter needs to be added.
• Steps in electrophoresis:
10.3 Gel electrophoresis o DNA extracted from anything that contains cells such
• A technique used to separate different molecules. as, root of hair, blood splatter, saliva and so on
o PCR is used to increase number of DNA
• A mixture of molecules is placed into wells cut into
o DNA cut into fragments using restriction endonuclease
agarose gel and applying an electric field.
o DNA is placed on agarose gel and current is applied
o Fragments travel towards anode, shorter fragments
traveling further/faster, than longer ones
o To make fragment visible:
▪ Place absorbent paper (nitrocellulose paper) on gel to
transfer fragment on it
▪ Heat the paper to separate both DNA strands
PAGE 40 OF 44
 CIE A2-LEVEL BIOLOGY//9700
▪ Add probes (short sequence of single strand), which o Fluorescent patches show hybridisation has taken
form complementary base pairing with VNTR regions place
▪ Probes also contain radioactive isotope which, when o Red tags indicate the gene probe is present in species
placed on an X-ray film, emits radiation, making the A
film go dark o Green tag indicates the gene is present in species B
▪ The dark strips on the film match position of o Yellow tag indicates the gene is present in both
fragment on gel species
▪ Alternatively, label probes with fluorescent stains • Microarray is then scanned using laser scanner and read
that fluoresce when UV light is shone using a computer. Data stored in computer indicates
which genes are present in which species.
10.5 Polymerase Chain Reaction (PCR)
• Is a method for rapid production of a particular fragment
of DNA to produce a very large number of copies
• Steps involved in PCR
o DNA is denatured by heating to 95 𝑜𝐶 and double helix
splits into two strands
o Annealing: Attaching primer onto ends of DNA after
cooling to about 65 𝑜𝐶 (primer is short sequence of
complimentary DNA)
To Identify the genes present that are being expressed:
o Elongation: Taq polymerase adds free nucleotides
• The mRNA is reverse transcribed to form cDNA
onto primer at 72 𝑜𝐶 to complete new DNA strand
• PCR can be done if cDNA is in low quantity
o This process is then repeated many times, at each time
• The same process as above can be used
doubling amount of DNA produced (exponential inc.)
• The fluorescence in the microarray indicates that those
• 𝑻𝒂𝒒 polymerase is used because:
genes were being transcribed and their intensities
o It is not easily destroyed by denaturing so doesn’t
indicate the activity of each gene
have to be replaced every cycle
o High optimum temperature: so temp. does not have to 10.7 Bioinformatics
be below (65 𝑜𝐶 ), hence faster rate of reaction
Bioinformatics is the collection, processing and analysing
of biological information & data using computer software
10.6 Microarrays
• Bioinformatics combines biological data with computer
• Tool to identify the genes present in an organism’s
technology and makes links
genome, which genes are being expressed and the level
• Databases hold gene sequences, complete genomes,
of activity
amino acid sequences and protein structures
• It could also be used to compare genes present in two
• Gene sequencing is the order of base pairs in sections of
different species
DNA, allowing genomes of many species to be published
• Microarray is a collection of genes, each in placed in
• Researches can use these databases to find similarities
depressions on a small chip/ slide
between the sequence of what they are studying and of
Process:
saved sequences in the databases
• DNA is collected from each species, cut up into different
• Sequences can be matched and degree of similarity
fragments and denatured to give lengths of single-
calculated, this can show if there is common ancestry
stranded DNA
• Information stored in database about plasmodium
• DNAs are labelled with fluorescent (eg species A = red,
allows us to find new methods to control it eg providing
species B = green) and mixed together allowing to
valuable information in the development of vaccines
hybridise with the probes on the microarray
• DNA that does not bind to the microarray is washed off
• Microarray is inspected using UV light

PAGE 41 OF 44
 CIE A2-LEVEL BIOLOGY//9700
10.8 Producing Human Proteins by GE • They are then cultured in fermenters, and so they
o Insulin produce the protein
o Factor 𝑉𝐼𝐼𝐼 - blood clotting protein • Protein is extracted, purified and regularly injected to
o Thyroid stimulating hormone patients
o Human growth hormone • Before recombinant factor VIII, it came from blood
• The general advantages of producing the proteins by donors and caused risk of infections eg HIV
genetic engineering is that:
o Simple nutritional requirement 10.9 Genetic Screening
o Large volume of product produced Genetic screening is the analysis of a person’s DNA to
o Production facilities do not require much space and so check for the presence of a particular allele for breast
can take place all around the world cancer, Huntington’s disease (late-onset disease), Sickle
cell anaemia, cystic fibrosis, haemophilia and etc.
o No risk of infection e.g. HIV from blood donation
• Adult woman can screen for faulty alleles of the genes
o Less ethical issues as blood need not be extracted
BRCA-1 and BRCA-2 which increases chances of breast
from animals or donors.
cancer
• Disadvantages: bacteria don’t modify their proteins the
• Preimplantation genetic diagnosis (PGD): At the 8 cell
same way eukaryotes do since Golgi bodies are absent.
stage during an IVF, one cell can be removed and
Insulin
checked for diseases; if embryo healthy, then implanted,
• In the past, diabetics were treated with insulin extracted
if not it is discarded
from pancreases of pigs or cattle
• Amniocentesis: performed at 15 weeks, a sample of
• Gene technology made it possible to synthetically make
amniotic fluid obtained and cells checked for any genetic
our own insulin
abnormalities
• So the advantage is that we now have a reliable supply
• Therapeutic abortion is terminating pregnancies for
of insulin available to the increasing demand
medical reasons and having advice from professionals
• GF insulin is identical to human insulin unlike insulin
• Parents decide to have abortions even if the defect is
previously extracted from cows
minor and child could have normal life
Method of insulin production:
• mRNA from human pancreatic 𝛽 cells are extracted • People that are diagnosed with the disease may never
develop it but would have to live with the fear of
• mRNA is incubated with reverse transcriptase producing
knowing it may start at any time (eg Huntington’s)
single stranded cDNA
• Parents also abort due to the sex of their child, and use
• DNA polymerase is used to convert into double strand
PDG to select the sex of the embryo. This preselection,
• Insulin gene (cDNA) is then inserted into a plasmid to
amongst others mentioned above, are considered
transform the bacterium
unethical.
• The bacteria can now produce insulin, so they are grown
• Could lead to the birth of designer babies where parents
in large fermenters and insulin is extracted and purified
select other aesthetically pleasing traits, also unethical
Reason why mRNA is more suitable than DNA extraction:
• mRNA is only from gene coding for insulin, whereas DNA
10.10 Types of Vectors
has all genes and so you must locate and extract gene
1. Viruses
• Restriction enzyme would be needed for DNA extraction
2. Naked DNA
• Large number of mRNA that code for insulin
3. Liposomes
Factor 𝑽𝑰𝑰𝑰
Viruses
• This is a protein that is essential for blood clotting,
• Retroviruses insert their genes into host randomly, so
people who do not have it are said to be haemophilic
they may insert it within a gene, or even worse into the
Method of Factor 𝑽𝑰𝑰𝑰 production:
regulatory gene and so can cause cancer
• Human gene inserted into hamster kidney and ovary
• Lentiviruses also insert genes randomly, however, they
cells
can be modified to inactivate replication

PAGE 42 OF 44
 CIE A2-LEVEL BIOLOGY//9700
10.11 Diseases and Gene Therapy
• Severe combined immunodeficiency (SCID): the inability
to produce the enzyme adenosine deaminase (ADA)
which helps detoxify the immune system. Without it, the
immune system is crippled, and sufferers usually die in
infancy from common infections.
o Children are isolated inside plastic bubbles to protect
from infections.
o Gene therapy used to introduce normal alleles of ADA
gene, using retroviruses at foetal stage. (Regular
transfusions were necessary)
• Inherited eye disease this is a form of hereditary
blindness in which retinal cells die off gradually from an
early age
Gene Therapy
• Is the altering of a genotype and inserting the normal
allele into the appropriate cells using a vector, producing
a functional recombinant DNA
• Eg the CFTR gene in cystic fibrosis is usually the cause of
a mutation of a deletion of 3 bases, so in theory inserting
normal dominant allele would transcribe the normal
protein
Cystic Fibrosis
• Cystic fibrosis is caused by a recessive allele that codes
for a transport protein called CFTR, causing the
production of abnormal thick mucus that is difficult to be
removed
• Other body parts such as pancreatic duct can become
blocked as well as reproductive ducts causing infertility
• CFTR effects on lungs:
o Due to mucus not moving effectively by cilia, bacteria
and dust accumulate, causing infections
o Reduces gaseous exchange, by making it a longer
diffusion pathway
o Causes difficulty in breathing
o Lungs may be scarred
• The CFTR gene normally codes for a transport protein
that allows chloride ions to pass out of cell
PAGE 43 OF 44
• Chloride ions are essential to be transported out so that
they cause concentration gradient outside, hence
causing water to move out of cells by osmosis
• The water mixes with the mucus making it easy for
removal by the sweeping movement of cilia
• The recessive allele codes for a faulty version of this
protein, not allowing cl- ions to pass out of the cell, so
water doesn’t move out and mucus remains thick.
• Vectors used for epithelial cells to take up gene:
o Liposomes in aerosol sprays
o Viral delivery by retrovirus/ adenovirus
o Naked DNA for direct delivery
• However, problems occur in practical situation such as:
o Allele needs to get into as many cells throughout
respiratory system, including cells that divide.
o Short natural lifespan; effects only last for a few days
o Low uptake by target cells
o Only target lung cells at this time
o Side effects such as infections caused by the virus
o However naked DNA is used (DNA directly inserted
into tissues) to prevent problems associated with
vectors.
• The advantages on the other hand are:
o No physiotherapy/antibiotics are needed
o Less time consuming than other types of treatments
10.12 Genetically Modified Plants
Herbicide resistant crops
• Growing herbicide resistant crops allows you to spray
herbicide after seed has germinated, killing weeds that
would otherwise compete for space, light and water
• Vector used: Agrobacterium plasmids
• Gene is taken up by plant cells to form a callus. The
callus is then grown under ideal conditions to form a
GMO plant
• Example: sugar beet
• This increases the yield of crop however; it has
disadvantages such as:
o Genetically modified plants become agricultural weeds
o Pollen will transfer into the wild, producing off-spring
that are invasive weeds
o Herbicide resistant weeds will evolve due to the usage
of same herbicide and so mutate
Insect resistant crops
• This is another important development that allows
plants to be protected against attack by insects
 CIE A2-LEVEL BIOLOGY//9700
• Vector used: Bt (a Bacillus bacterium) • Can lose traditional varieties with their desirable
• Bt gene is inserted into the plant. It produces crystal background genes, hence would have to make
proteins which kill insects when taken up programmes of growing and harvesting them. Also
• Examples: Bt maize, Bt cotton forcing us to setup seed bank to preserve them
• Again, crop yield increases however its disadvantages • No bioaccumulation
are: • Allows non leguminous plants to fix nitrogen
o Evolution of resistance by insect pests • Increased yield in insecticide and herbicide resistant
o A damaging effect on other species of insects crops
o The transfer of the added gene to other species of • Increased quality/ taste
plant. • Flavr Savr tomatoes can ripen on vines, reducing food
Golden Rice waste in supermarkets
• Golden rice is meant to be healthier than white rice due
to increased Vitamin A content, as its deficiency can
cause blindness and the
immune deficiency syndrome
that in turn causes a high level
of mortality in children in
developing countries
• Pro-vitamin A carotenoids are present in the aleuronic
layer of normal rice grains however; this layer is usually
removed so that it does not go rancid quickly
• Therefore, projects to produce rice that contain
carotene in the endosperm were undertaken producing
genetically modified golden rice
• Vector used: Agrobacterium
• First generation of golden rice used genes from daffodils
• Second generation of golden rice uses genes from maize
Disadvantages to growing Golden Rice would be:
o GM seed could be difficult for farmers in developing
countries to obtain, as it cannot be replanted
o High cost of buying GM seed, so also expensive for
people to buy
o May not grow well in all conditions
o Might reduce efforts to relieve poverty

10.13 Social Implications of Using GM

Organisms in Food Production
• Modified crop plants can become agricultural weeds
• Introduced genes may be transferred by pollen to wild
offspring and so become more invasive
• Can be transferred by pollen to organic certified farms
• Hazard to humans as they can produce allergies
• The herbicide can leave toxic residue on the crop
• Growers need to buy seeds each season which is
expensive

PAGE 44 OF 44