unit 4 notes

by : Abdalrhman fayez

5.1 understand the overall reaction of photosynthesis as requiring

energy from light to split apart the strong bonds in water
molecules, storing the hydrogen in a fuel (glucose) by combining it
with carbon dioxide and releasing oxygen into the atmosphere

- require light energy photosynthesis

- break bond in antimolecule
- hydrogen pumped across thylakoid membrane
-carbon fixation
- O2 diffuses out of stomata

5.2 understand how photophosphorylation of ADP requires energy

and that hydrolysis of ATP provides an immediate supply of energy
for biological processes-

Synthesising ATP is a condensation reaction

- ATPase enzyme catalyses this reaction
- The energy needed to drive synthesis of ATP usually comes from
catabolic break down reaction or redox reactions
- ATP molecules provide an immediate supply of energy for your cells,
ready to use when you need it
 5.3 understand the light-dependent reactions of photosynthesis,
including how light energy is trapped by exciting electrons in
chlorophyll and the role of these electrons in generating ATP,
reducing NADP in cyclic and non-cyclic photophosphorylation and
producing oxygen through photolysis of water

- Redox reactions in ETC release a small amount of energy which is used

to drive synthesis of ATP molecule
- when a photon of light hits chlorophyll molecule, the energy
transferred to the electrons of the chlorophyll molecule
- The electrons are excited and are raised to higher energy levels
- The electron is accepted by carrier molecule and results in making of
ATP through cyclic and non-cyclic phosphorylation
-both processes occur at the same time
- ATP formed as excited electrons transferred along an ETC
- IN N.C.PH, NADP is also produced
 5.4 (i) understand the light-independent reactions as reduction of
carbon dioxide using the products of the light-dependent reactions
(carbon fixation in the Calvin cycle, the role of GP, GALP, RuBP and
RUBISCO)

- Occurs in stroma of the chloroplast

- Each stage of the cycle is controlled by enzymes
- CO2 combine with RuBP and CO2 is fixes-> Rubisco enzyme
- 6 C compound formed which separates into 2 molecule of 3GP
- 3GP reduced to 3GALP
- reduced NADP is reducing agent
- ATP break down gives energy required

5.4 (ii) know that the products are simple sugars that are
used by plants, animals and other organisms in respiration
and the synthesis of new biological molecules
(polysaccharides, amino acids, proteins, lipids and nucleic
acids)

- Much of the 3 carbon GALP is used to replace RuBP

- However, some GALP is used to make glucose in gluconeogenesis
- Glucose could be made into sucrose for transport round the plant
- Glucose could be made into starch for energy storage
- Glucose could be made into cellulose for structural support
 5.5 understand the structure of chloroplasts in relation to their role
in photosynthesis

- Consists of an inner and outer membrane, with a chloroplast envelope

between them
-There is a system of membrane inside chloroplast that are arranged in
layers known as Grana.
- A granum is made up of layers of membrane known as thylakoid
- green pigment found in thylakoid
- pigment molecule arranged in 2 photosystems
- grana joined together by lamellae surface area
- lamellae inc sa for light absorption
- stroma contain enzymes for photosynthesis

5.6 understand what is meant by the terms absorption spectrum

and action spectrum

Absorption spectrum: describes the different amounts of lights and

different wavelengths that a photosynthetic pigment absorbs

Action spectrum: rate of photosynthesis according to wavelength of light

 5.7 understand that chloroplast pigments can be separated using
chromatography and the pigments identified using Rf values

- You can extract pigment by grinding up leaves with propanone then

filtering
- use silica gel
- pigments travel up solid medium at different speeds and are readily
separated using a suitable solvent
- You can obtain Rf values and compare to Rf values of known pigment

5.9 (i) understand the relationship between gross primary productivity (GPP), net
primary productivity (NPP) and plant respiration (R)

- NPP = GPP - R
- GPP-> rate at which plants make new material by photosynthesis
- units kJm-2yer-1
- NPP-> energy store/ available to the next trophic level

5.10 know how to calculate the efficiency of biomass and energy

transfers between trophic levels

- energy used/total energy x 100

 5.11 The difference between population community and ecosystem

- population: A group of organisms of the same species living and

breeding together in a habitat

- Community: all the population living together in a habitat at any one

time

- Ecosystem: An environment containing all organism interacting with it,

biotic and abiotic factor

5.12 understand that the numbers and distribution of organisms in

a habitat are controlled by biotic and abiotic factors

Abiotic factors:
- light, temperature, wind and water currents, water availability, oxygen
availability, edaphic factors

Biotic factors:
- predation, finding a mate, territory, parasitism, and disease
 5.13 understand how the concept of niche accounts for the
distribution and abundance of organisms in a habitat

- Abundance- relative representation of species in a particular

ecosystem

- Distribution- where a species of an organism is found in an

environment and how it is arranged....

5.14 understand the stages of succession from colonisation to the

formation of a climax community

1- starts off with empty inorganic surface

2- colonisation- opportunists/pioneer species appear
3- penetration of rock surface - acids/ root hairs and hyphae
4- formation of hummus and inorganic rock grains form soil
5- conditions more hospitable, biodiversity increases
6- new species outcompete pioneer species
7- climax community- self sustaining, stable
 5.16 understand the different types of evidence for climate change
and its causes, including records of carbon dioxide levels,
temperature records, pollen in peat bogs and dendrochronology,
recognising correlations and causal relationships

1- Temperature records
-> use oxygen isotopes in melted ice to reflect air temp and time ice
layer formed

2- Dendrochronology
-> use of tree ring growth to date past events
-> count of rings can find age of tree approx.
-> photosynthesis occurs and affects growth

3- Peat bog records

-> peat preserves pollen grains, pores and mass tissues
-> as the type of plant that can grow in an area are affected by climate,
the pollen/moss record can give a clear reflection of how the climate
changed with time.
-> depends on prevailing conditions

increasing reliability of data

- use of dating, compare to calibration
 5.16

Causation vs correlation

causation- change in one variable causes change in another variable

correlation- tendency for two sets of data to vary together

5.17 understand the causes of anthropogenic climate change,

including the role of greenhouse gases in the greenhouse effect

1- Greenhouse effect
- short wave IR penetrate atmosphere to reach surface of earth
- some IR passes back through atmosphere
- Earth reflects long wavelength IR
- Greenhouse gases absorb IR and reradiate it

- burning of fossil fuels

- use of car
-deforestation
 5.18 understand how knowledge of the carbon cycle can be applied
to methods to reduce atmospheric levels of carbon dioxide

- Use of carbon sinks-carbon removed from atmosphere and is locked

there
- can be bodies of living organisms or rocks
-use of carbon neutral material
- use of biofuels
- use of renewable energy resources
- reforestation

5.19 (i) understand that data can be extrapolated to make predictions and that these
are used in models of future climate change

- we can extrapolate data and use to make predictions

5.19 (ii) understand that models for climate change have

limitations

- it is impossible to tell the exact impact of co2 on global warming

-impossible to predict exact impact of global warming on particular
aspect of world climate
- extrapolation from past don’t take into account change in technology
 5.20 understand the effects of climate change (changing rainfall
patterns and changes in seasonal cycles) on plants and animals
(distribution of species, development and lifecycles)

1. change in temperature seasons

-> temp has an effect on enzyme activity
-> Q10
-> can affect rate of growth and reproduction
-> can affect breeding and life cycles

2. Rainfall changes
-> can affect society and population
-> drought can mean organisms will struggle and people will find it
impossible to grow enough food to survive

3. Change in species distribution

-> animals survive easier to change as they can move whereas plants
cant
-> cant survive and reproduce

5.21 understand the effect of temperature on the rate of enzyme activity and
its impact on plants, animals and microorganisms, to include Q10

- temp affect enzyme activity

- q10
- 0-40C , any 10 degree rise in temp doubles ror
- optimum temp and enzyme denaturation
- affect rate of growth and reproduction
 5.23 understand how evolution (a change in allele frequency) can
come about through gene mutation and natural selection

- mutation
- advantageous allele favoured
- due to selection pressure
- survive and reproduce
-allele passed on to offspring
- inc in allele freq over future generation

5.24 understand how isolation reduces gene flow between

populations, leading to allopatric or sympatric speciation

1. Allopatric speciation
- occurs when population are geographically isolated
- the plant and animal in these isolated populations will breed
- selection pressure will drive them to adapting to diff conditions

2. Sympatric speciation
- occurs when organisms are reproductively isolated by mechanical,
seasonal or behavioural changes
-reproductively isolated
- cant interbed to produce fertile offspring
-diff courtship behaviours
 5.25 understand the way in which scientific conclusions about
controversial issues, such as what actions should be taken to
reduce climate change, or the degree to which humans are
affecting climate change, can sometimes depend on who is
reaching the conclusions

- politicians usually make these decisions.

-influenced by pressure groups and lobbyists who will be biased by their
own interests.
- environmental campaigners exist?....
-politicians make decisions based on short term gains when they seek re
election.

5.26 understand how reforestation and the use of sustainable

resources, including biofuels, are examples of the effective
management of the conflict between human needs and
conservation
- sustainable: won’t run out avail to future generations

- use of biofuels
-> they use products from those plant as fuel
-> carbon neutral
-> takes up space to grow plant so threatens food production

- use of renewable energy resources

-reforestation

6.1 understand the principles and techniques involved in culturing

microorganisms, using aseptic technique

- aseptic technique:
-> nutrient broth or nutrient agar
-> inoculating loop place in a Bunsen flame
-> use bench coat, sterilize area using disinfectant
-> tape container leave slightly open

- Selective medium
-> only a select group of microorganisms would grow
-> can identify mutant strains
-> can identify genetically modified microorganisms
-> need to know aerobic/anaerobic, nutritional requirement, add dye for
a colour change- antibiotic/antifungal
-> can be isolated or cultured
 6.2 understand the different methods of measuring the growth of
microorganisms, as illustrated by cell counts, dilution plating, mass
and optical methods (turbidity)

1. Haemocytometer
- dilute sample of nutrient broth by half with an equal volume of trypan blue
- stain dead cells
-view and count cells on microscope
-take at regular time interval

2. Optical method
- turbidity
- less light can pass through
- produce calibration curve
- grow control culture at regular time intervals

3. Dilution plating
- used to find total viable cell count
- dilution helps with clumping
- no of colonies x d.f

4. Area and mass of fungi

- measure diameter- compare growth rates in diff conditions
-inoculate petri dish with same growth medium and same no of fungal spores
-culture petri dish at different temp
- after a specific time, measure diameter of each colony and find mean

5. Dry mass
- centrifuge/filter to separate fungi from liquid
- dry material until u find no loss of mass
- conditions that give greatest dry mass are optimum
 6.3 understand the different phases of a bacterial growth curve
(lag phase, exponential phase, stationary phase and death phase)
and be able to calculate exponential growth rate constants

1. Lag phase
- where bacteria are adapting to their new environment and are not
reproducing at their maximal rate

2. Log/exponential phase
- rate of bacterial reproduction is close to or at its theoretical maximum
rate

3. Stationary phase
- total growth rate is zero and number of new cells formed by binary
fission is equal to the number of cells dying

4. Death/decline phase
- reproduction has almost stopped and the death rate of cells is
increasing

6.5 (i) be able to compare the structure of bacteria and viruses

(nucleic acid, capsid structure and envelope) with reference to
Ebola virus, tobacco mosaic virus (TMV), human immunodeficiency
virus (HIV) and lambda phage (λ phage)
Structure of bacteria
- peptidoglycan cell wall
- nucleoid
- 70s ribosome

Virus
-capsid
- envelope
- VAP
- Strand of DNA/RNA

DNA virus
- viral DNA template for both new viral DNA and mRNA needed to
synthesize viral proteins
- E.g. lambda phage

RNA virus
- more likely to mutate
-ssRNA
-e.g. Ebola , TMV

Retrovirus
-protein capsid and a lipid envelope
- ssRNA controls synthesis of reverse transcriptase
- make DNA molecule corresponding to a viral genome
- e.g. HIV
 6.5 (ii) understand what is meant by the terms lytic and latency

lytic
- viral genetic material replicates independently of the host DNA
- mature viruses are made and host cell burst
- virus is disease causing

latency
- part of lysogenic pathway
- non-virulent

- 6.6 understand how Mycobacterium tuberculosis causing

symptoms that may result in death

respiratory system
- primary infection->
- bacteria inhaled into the lungs will multiply slowly, causing no obv
symptoms.
- there would be localized inflammatory response forming a tubercule
- some bacteria survive primary infection because of the thick waxy
outer layer that protects them from the enzyme of macrophages
- the bacteria is dormant until immunosuppression occurs
- the bacteria then cause active TB
- DNA of bacteria passed on, grow and reproduce rapidly
- Tuberculosis’s target T cells, reduced the production of antibodies.
- TB causes death because lack of oxygen from the air due to damaged
lungs or because organs fail due to lack of nutrition, or vulnerable to
opportunistic infections
 6.7 (i) know the major routes pathogens may take when entering the body

Methods of spread:
- Vectors
- Inhalation
- Ingestion
- fomites
- direct contact
- inoculation

6.7 (ii) understand the role of barriers in protecting the body from
infection, including skin, stomach acid, and gut and skin flora

1- Epithelial defences and sebum

2- Lysozymes
3- Mucus and cilia
4- Gut flora
5- hCL in stomach
6- skin flora
7- saliva
8- blood clotting
 6.8 understand the non-specific responses of the body to infection, including
inflammation, lysozyme action, interferon and phagocytosis

1. Inflammation
-localized infection
- when tissue is damaged, mast cells and basophils release histamines
- histamines cause vasodilation and inc permeability of blood vessels
-raised temp reduce reproduction rate of pathogen
- inc in permeability means antibodies are forced out of capillaries
- antibodies disable pathogen and the macrophage and neutrophils
destroy them by phagocytosis

6.8 Lysozyme action

- when phagocytes engulf a pathogen, it is enclosed in a vesic;e called

phagosome.

-phagosome fuses with lysosome

- lysozyme break down the pathogen

- after phagocyte has engulfed a pathogen, it produces cytokines so

stimulate other phagocytes to move to site of infection.
 6.8 interferon

- effective only against viruses

- cells invaded by viruses produce interferon
- interferon inhibit viral replication within the cells
- interferon diffuses from the cell to surrounding cells
- interferon binds to receptors in csfm of uninfected cells
this makes cells resistant to infection by viruses
- hence intfrn prevent infection of more cells after lysis

6.8 phagocytosis

- macrophages and neutrophils

- phagocyte engulf pathogen and form phagosome
- phagosome fuses with lysosome
- lysozyme in lysosome break down pathogen
- antigen presented on csfm, APC formed
- produce cytokine to stimulate other phagocyte to site of infection
 6.9 understand the roles of antigens and antibodies in the body's
immune response including the involvement of plasma cells,
macrophages and antigen-presenting cells

Humoral response
- for antigens found outside body and APC in body

1. T helper activation
- bacterium engulfed by macrophage, macrophage presents
antigen form bacterium on MHC, becomes APC. A macrophage
APC binds to T helper cell. Once T cell is activated, it divides to
form T memory cells and active T helper cells.

2. Effector stage
- antigen binds to B cell with complementary receptior
- The B cell engulfs bacterium by endocytosis and enzymes
break it down to leave antigen fragments
- B cell becomes APC
- Activated T helper cell bind to APC, produces cytokine that
stimulate B cell
-B cell divide to give B memory and B effector cells
- B effector cells differentiate into plasma cells
- Plasma cells secrete antibodies, these bind to antigen
 6.10 understand the differences between the roles of B cells (B
memory and B effector cells), and T cells (T helper, T killer and T
memory cells) in the host's immune response

B cells
- produced and mature in bone marrow
- B effector cell divide to form plasma cell clines
-plasma cells produce specific antibodies
- B memory cells - faster and stronger response if reencountered
They develop in the bone marrow.
These cells are activated on their encounter with foreign agents. These foreign particles
act as foreign markers.
The B-cells immediately differentiate into plasma cells which produce antibodies specific
to that foreign particle or so-called antigen.
These antibodies attach to the surface of the antigen/foreign agent.
These antibodies detect any antigen in the body and destroy it.
The immunity dependent on B-cells is called humoral immunity.

T cells
- produced in marrow but mature in thymus gland
- T killer cells produce chemicals to destroy infected body cells
- T helper cells activate plasma cell to produce antibodies against antigen and secrete
opsonins to label pathogen for phagocytosis
- T memory cells - form large clone of T killer cells- quickly destroy pathogen
They originate in the bone marrow and develop in the thymus.
T-cells differentiate into helper cells, cytotoxic cells, and regulatory cells. These cells are released into the
bloodstream.
When these cells are triggered by an antigen, helper T-cells release cytokines that act as messengers.
These cytokines initiate the differentiation of B-cells into plasma cells which release antibodies against
the antigens.
The cytotoxic T-cells kills the cancer cells.
 6.11 understand how individuals may develop immunity (natural,
artificial, active and passive

natural activity immunity-body actively makes antibodies

natural passive immunity- preformed antibodies passed from mother to

fetus- gives temporary immunity until the immune system develops-
short-lived.

artificial active immunity-small amount of detoxified/deas/attenuated

pathogen are used as vaccines so antibodies are made and memory cells
produced.

artificial passive immunity- antibodies from one individual are injected

into another individual. short-lived. prevent the development of disease
and death.
 6.12 understand how the theory of an 'evolutionary race' between
pathogens and their hosts is supported by evasion mechanisms
shown by pathogens

- there is an evolutionary race between pathogens and their host

- bacteria keep evolving resistance to drugs
- an antibiotic is only effective if the microorganism has a binding site for
the drug
-a mutation can occur during bacterial reproduction
-as a result of natural selection, advantageous mutations become more
common
- the bacterial population becomes more resistant to the drug.
- mutation can also create gene of the antibiotic destroying enzyme

6.13 understand the difference between bacteriostatic and bactericidal antibiotics

Bacteriostatic- inhibits the growth of bacteria

- protein synthesis inhibit/ prevent transcription of microbial genes
- so protein production is affected

Bactericidal- kill bacteria

- destroy peptidoglycan cell wall so cell bursts
- used in severe infections more
 6.15 know how an understanding of the contributory causes of
hospital-acquired infections has led to codes of practice regarding
antibiotic prescription and hospital practice that relate to infection
prevention and control
- mRSA and c. difficile more common infection

1. control use of antibiotic by

-> taking only when neccessary
-> course should be completed
-> dont use multiple antibitoic- encourage MDR

2. Hand washing and hygeine practice

3. Isolation of patient

4. prevent infection from coming into hospital

5. Monitoring level of HAI

6.16 know the role of microorganisms in the decomposition of organic

matter and the recycling of carbon

- bacteria and fungi

- they feed on faces and dead bodies, digest and use nutrient fro
respiration
- they release waste products, provide nutrients that plants can use
once more
- the carbon cycle is part of nutrient recycling
- microorganism produce cellulase enzyme and break down cellulose in
plant cell wall to produce sugar
- decomposers release carbon into atmosphere
 6.17 know how DNA can be amplified using the polymerase chain
reaction (PCR)

- 1.reactants placed in a PCR machine

-2. 90-95C for 30 seconds- DNA strands separate.

-50-60C for 20 seconds: primers bind to DNA strands.

- 75C for at least a minute: DNA polymerase builds up complementary

strands of DNA.

6.18 know how gel electrophoresis can be used to separate DNA

fragments of different length

- dna fragments place in wells in an agarose gel medium in a buffering solution to keep
pH constant.

- add dye to gel so it can reveal the band of DNA.

- An electric current passes through the apparatus

- DNA fragments move towards positive anode because of the negative charge on the
phosphate groups of the DNA backbone.

- fragments move at different rates according to size and charge.

- place plate under short UV light

- use it in forensic science, familial testing and classification of organisms.

 6.19 understand how DNA profiling is used for identification and
determining genetic relationships between organisms (plants and
animals)

- The DNA fragments which are revealed in DNA profiling are unique.

- we can use simlarity of patterns to identify relationships between

individuals and between species.

-compare DNA bands

- coding parts pf DNA are used

- genes coding for proteins that are universal are best (RNA polymerase)

6.20 understand how to determine the time of death of a mammal

by examining the extent of decomposition

- temperature and level of exposure affect

- l.o.e- available to flies and other decomposers
 6.20 understand how to determine the time of death of a mammal
by examining the stage of succession

1. colonisers- anaerobic bacteria

2- joined by blowflies- at first lay eggs, the maggots hatch and begin
feeding on tissues and break them down. the maggots pupate, turn into
flies and start the cycle again.

3-beetles lay eggs on decaying body- their larvae feed on maggots.

4- parasitic wasps, early colonisers begin to dissapear

5- beetle species feed on remain of muscle tissues

6.20 understand how to determine the time of death of a mammal

by examining forensic entomology

- life cycle of blowflies

- at 21 C
-1st larval stage-24hours to
- 2nd larval stage- 22 hours to
- 3rd larval stage- 130 hours to
- pupa - 143 hours to
- adult- 23 hours to
- 1st larval stage

- blowlfies lay eggs in body openings- can help estimate time of death
 6.20. understand how to determine the time of death of a mammal
by examining body temperature

- fat levels, mode of death, surrounding tmeperatures, SA:vol RATIO, clothing and
covering affect rate of colling.
- u can draw a cooling curve

6.20 understand how to determine the time of death of a mammal

by examining the degree of muscle contraction

- Rigor mortis
- muscle cells have large stores of ATP
- so they resipire anaeorbically for some time after death
- after death muscle cells use all of ATP
- muscle fibres are permanently contracted
- body is rigid
- affected by amount of ATP stored in muscles and temperature
(enzymes)

dendrochronology

studying the size of tree rings is called dendrochronology.

If the climate is 1 -----Jwarmer and wetter then the rings are wider.
We can look at tree ring widths and telll climate past and present
 peat bogs

- pollen grains are preserved in peat bogs

- by sampling at different levels in peat are sampling at different ages
-analysis of pollen can tell us which plants were growing
- what the climate was like when peat was formed

ice cores

air trapped in ice analysed

co2 and temp levels in past

global warming effect on species distribution

- migration
-outcompete native spciees
- extinction

changes to development

-can affect sex of young that hatch from eggs

so change sex ratio
 changes in lifecycle

- insect may get through their life cycles more quickly and be ready to
feed before the plants they feed are mature

- plants flower earlier

extent of decomposition

-bodies usually follow a standard pattern of decay.

-Enzymes in the gut start to break down the wall of the gut and then the
surrounding area.
-As cells die they release enzymes which help to break down tissues.
T- he signs of decomposition, such as discoloration of the skin and gas
formation, combined with information about environmental conditions
allow time of death to be estimated.

extent of decompostion

-bodies usually follow a standard pattern of decay.

-Enzymes in the gut start to break down the wall of the gut and then the
surrounding area.
-As cells die they release enzymes which help to break down tissues.
T- he signs of decomposition, such as discoloration of the skin and gas
formation, combined with information about environmental conditions
allow time of death to be estimated.
Term Meaning

Pathogen A disease-causing organism, including bacteria,

Antigen Molecule that stimulates an immune response

Innate immune
system Non-specific immune system

Adaptive
immune system Antigen-specific immune system

Specialized Y-shaped protein that tags antigens for

Antibody destruction

White blood cells that produce antibodies and aid

B cells in immunological memory

White blood cells specialized to assist B cells

(helper T) and others directly kills infected cells
T cells (killer T)

Humoral Adaptive immune defense depending on the action

immunity of antibodies

Cell-mediated Adaptive immune defense in which foreign cells are

Immunity destroyed by T cells

Nonliving particle containing protein and

Virus DNA/RNA that can infect a living cell

A killed or weakened form of a pathogen that

Vaccine produces immunity when injected into the body
Nonspecific defense: the innate immune
system
The human body has a series of nonspecific defenses that make up
the innate immune system. These defenses are not directed against any
one pathogen but instead, provide a guard against all infection.

First line of defense

The body's most important nonspecific defense is the skin, which acts as
a physical barrier to keep pathogens out. Even openings in the skin (such
as the mouth and eyes) are protected by saliva, mucus, and tears, which
contain an enzyme that breaks down bacterial cell walls.

Second line of defense

If a pathogen does make it into the body, there are secondary nonspecific
defenses that take place.
 Image showing white blood cells releasing chemicals to induce
inflammatory response
Inflammatory response. Image from OpenStax, CC BY 4.0

An inflammatory response begins when a pathogen stimulates an

increase in blood flow to the infected area. Blood vessels in that area
expand, and white blood cells leak from the vessels to invade the infected
tissue. These white blood cells, called phagocytes engulf and destroy
bacteria. The area often becomes red, swollen, and painful during an
inflammatory response.

When a pathogen has invaded, the immune system may also release
chemicals that increase body temperature, producing a fever. Increased
body temperature may slow or stop pathogens from growing and helps
speed up the immune response.

Specific defense: the adaptive immune

system
When pathogens are able to bypass innate immune defenses,
the adaptive immune system is activated.

Cells that belong in the body carry specific markers that identify them as
"self" and tell the immune system not to attack them.

Once the immune system recognizes a pathogen as "non-self," it uses

cellular and chemical defenses to attack it. After an encounter with a new
pathogen, the adaptive immune system often "remembers" the pathogen,
allowing for a faster response if the pathogen ever attacks again.
Specific immune responses are triggered by antigens. Antigens are
usually found on the surface of pathogens and are unique to that
particular pathogen. The immune system responds to antigens by
producing cells that directly attack the pathogen, or by producing special
proteins called antibodies. Antibodies attach to an antigen and attract
cells that will engulf and destroy the pathogen.

The main cells of the immune system are lymphocytes known as B

cells and T cells. B cells are produced and mature in bone marrow. T
cells are also produced in bone marrow, but they mature in the thymus.

Humoral immunity
Humoral immunity relies on the actions of antibodies circulating
through the body.
Humoral immunity begins when an antibody on a B cell binds to an
antigen. The B cell then internalizes the antigen and presents it to a
specialized helper T cell, which in turn activates the B cell.

Activated B cells grow rapidly, producing plasma cells, which release

antibodies into the bloodstream, and memory B cells, which store
information about the pathogen in order to provide future immunity.

Cell-mediated immunity
Antibodies alone are often not enough to protect the body against
pathogens. In these instances, the immune system uses cell-mediated
immunity to destroy infected body cells.
T cells are responsible for cell-mediated immunity. Killer T cells
(cytotoxic T cells) assist with the elimination of infected body cells by
releasing toxins into them and promoting apoptosis. Helper T cells act to
activate other immune cells.

Vaccines
Vaccines work by taking advantage of antigen recognition and the
antibody response. A vaccine contains the antigens of a pathogen that
causes disease. For example, the smallpox vaccine contains the antigens
specific to smallpox. When a person is vaccinated against smallpox, the
immune system responds by stimulating antibody-producing cells that
are capable of making smallpox antibodies. As a result, if the body comes
into contact with smallpox in the future, the body is prepared to fight it.

Viral structure
Viruses are infectious particles that reproduce by hijacking a host cell
and using its machinery to make more viruses.
Diagram of a virus. The exterior layer is a membrane envelope. Inside the
envelope is a protein capsid, which contains the nucleic acid genome.
Image modified from Wikimedia, CC BY-SA 2.5

There are many kinds of viruses, differing in structure, genome, and host
specificity. However, viruses tend to have several features in common.
All viruses contain a protective protein shell, or capsid, that houses their
nucleic acid genome (either DNA or RNA).

Some viruses also have a membrane layer called an envelope that

surrounds the capsid.

Steps of viral infection

Viruses reproduce by infecting their host cells, providing instructions in
the form of viral DNA or RNA, and then using the host cell's resources to
make more viruses.
Steps of a viral infection, illustrated generically for a virus with a + sense
RNA genome.

1. Attachment. Virus binds to receptor on cell surface.

2. Entry. Virus enters cell by endocytosis. In the cytoplasm, the capsid

comes apart, releasing the RNA genome.

3. Replication and gene expression. The RNA genome is copied (this

would be done by a viral enzyme, not shown) and translated into
viral proteins using a host ribosome. The viral proteins produced
include capsid proteins.
 4. Assembly. Capsid proteins and RNA genomes come together to
make new viral particles.

5. Release. The cell lyses (bursts), releasing the viral particles, which
can then infect other host cells.

1. The virus recognizes and binds to a host cell via a receptor

molecule on the cell surface.

2. The virus or its genetic material enters the cell.

3. The viral genome is copied and its genes are expressed to make
viral proteins.

4. New viral particles are assembled from the genome copies and
viral proteins.

5. Completed viral particles exit the cell and can infect other cells.

Common mistakes and misconceptions

 Not all bacteria are pathogens. Most bacteria are actually
harmless and, in fact, we would not survive without them! Bacteria
help us digest food, produce vitamins, and act as fermenting agents
in certain food preparations.

Some bacteria also fill niches that would otherwise be open for
pathogenic bacteria. For example, the use of antibiotics can wipe
out gastrointestinal (GI) flora. This allows competing pathogenic
bacteria to fill the empty niche, which can result in diarrhea and GI
upset.
 Some diseases have been nearly eliminated through the use of
vaccines. However, this does not mean that we should stop
vaccinating against these diseases. Most of these diseases still do
exist in the human population, and without the continued use of
vaccines, people are at risk of getting and spreading the disease.

 Some people may think that vaccines provide permanent

immunity to a disease. For some diseases, a single vaccine is
sufficient, but for many diseases you must get vaccinated more
than once to be protected.

For example, the flu vaccine becomes less effective over time
because of how rapidly the flu virus mutates. Therefore, the flu
shot’s formulation changes each year to protect against specific
viruses that are predicted to be prominent each year.
Even bacteria can get a virus! The viruses that infect bacteria are
called bacteriophages, and certain bacteriophages have been studied in
detail in the lab (making them some of the viruses we understand best).

In this articles, we'll take a look at two different cycles that

bacteriophages may use to infect their bacterial hosts:

 The lytic cycle: The phage infects a bacterium, hijacks the

bacterium to make lots of phages, and then kills the cell by making
it explode (lyse).

 The lysogenic cycle: The phage infects a bacterium and inserts its
DNA into the bacterial chromosome, allowing the phage DNA (now
called a prophage) to be copied and passed on along with the cell's
own DNA.

Let's take a closer look at each of these cycles.

A bacteriophage is a virus that infects bacteria
A bacteriophage, or phage for short, is a virus that infects bacteria. Like
other types of viruses, bacteriophages vary a lot in their shape and
genetic material.

 Phage genomes can consist of either DNA or RNA, and can contain
as few as four genes or as many as several hundred^{1,2,3}1,2,3start
superscript, 1, comma, 2, comma, 3, end superscript.
 The capsid of a bacteriophage can be icosahedral, filamentous, or
head-tail in shape. The head-tail structure seems to be unique to
phages and their close relatives (and is not found in eukaryotic
viruses)^{4,5}4,5start superscript, 4, comma, 5, end superscript.
Bacteriophage infections
Bacteriophages, just like other viruses, must infect a host cell in order to
reproduce. The steps that make up the infection process are collectively
called the lifecycle of the phage.

Some phages can only reproduce via a lytic lifecycle, in which they burst
and kill their host cells. Other phages can alternate between a lytic
lifecycle and a lysogenic lifecycle, in which they don't kill the host cell
(and are instead copied along with the host DNA each time the cell
divides).

Let's take closer look at these two cycles. As an example, we'll use a
phage called lambda (\lambdaλlambda), which infects E. coli bacteria and
can switch between the lytic and lysogenic cycles.

Lytic cycle
In the lytic cycle, a phage acts like a typical virus: it hijacks its host cell
and uses the cell's resources to make lots of new phages, causing the cell
to lyse (burst) and die in the process.
The stages of the lytic cycle are:

1. Attachment: Proteins in the "tail" of the phage bind to a specific

receptor (in this case, a sugar transporter) on the surface of the
bacterial cell.

2. Entry: The phage injects its double-stranded DNA genome into the
cytoplasm of the bacterium.

3. DNA copying and protein synthesis: Phage DNA is copied, and

phage genes are expressed to make proteins, such as capsid
proteins.
 4. Assembly of new phage: Capsids assemble from the capsid
proteins and are stuffed with DNA to make lots of new phage
particles.

5. Lysis: Late in the lytic cycle, the phage expresses genes for proteins
that poke holes in the plasma membrane and cell wall. The holes let
water flow in, making the cell expand and burst like an overfilled
water balloon.

Cell bursting, or lysis, releases hundreds of new phages, which can find
and infect other host cells nearby. In this way, a few cycles of lytic
infection can let the phage spread like wildfire through a bacterial
population.
Lysogenic cycle
The lysogenic cycle allows a phage to reproduce without killing its host.
Some phages can only use the lytic cycle, but the phage we are following,
lambda (\lambdaλlambda), can switch between the two cycles.

[Do all phages use one of these two strategies?]

In the lysogenic cycle, the first two steps (attachment and DNA injection)
occur just as they do for the lytic cycle. However, once the phage DNA is
inside the cell, it is not immediately copied or expressed to make
proteins. Instead, it recombines with a particular region of the bacterial
chromosome. This causes the phage DNA to be integrated into the
chromosome.

[Is this true of all phages?]

Bacteriophage Structure

Phage have a very simple structure (Figure 1). Their genetic material is
contained in a prism shaped head, surrounded by a protein capsid. This is
connected to the elongated sheath (sometimes called the tail) by a neck or
collar region.

The sheath forms a hollow tube through which the viral DNA/RNA is
injected into the host cell and is surrounded by protective sheath proteins.
At the bottom of the sheath is the base plate to which the tail fibers
(normally six) that facilitate attachment to the host cell are attached.
Transition from lysogenic to lytic

If a bacterium containing prophage is exposed to stressors, such as UV

light, low nutrient conditions, or chemicals like mitomycin C, prophage
may spontaneously extract themselves from the host genome and enter
the lytic cycle in a process called induction.

This process, however, is not perfect and prophage may sometimes leave
portions of their DNA behind or take portions of host DNA with them
when they re-circularize. If they then infect a new host cell, they may
transport bacterial genes from one strain to another in a process called
transduction. This is one method by which antibiotic resistance genes,
toxin and superantigen-encoding genes and other virulence traits may
spread through a bacterial population.

You can take this video as example

https://youtu.be/hFwA0aBX5bE

To lyse or not to lyse?

How does a phage "decide" whether to enter the lytic or lysogenic cycle
when it infects a bacterium? One important factor is the number of
phages infecting the cell at once^99start superscript, 9, end superscript.
Larger numbers of co-infecting phages make it more likely that the
infection will use the lysogenic cycle. This strategy may help prevent the
phages from wiping out their bacterial hosts (by toning down the attack
if the phage-to-host ratio gets too high)^{10}10
What triggers a prophage to pop back out of the chromosome and
enter the lytic cycle? At least in the laboratory, DNA-damaging agents
(like UV radiation and chemicals) will trigger most prophages in a
population to re-activate. However, a small fraction of the prophages
in a population spontaneously "go lytic" even without these external
cues^{7,11}7,11start superscript, 7, comma, 11, end superscript.

Bacteriophage vs. antibiotics

Before antibiotics were discovered, there was considerable research on
bacteriophages as a treatment for human bacterial diseases.
Bacteriophages attack only their host bacteria, not human cells, so they
are potentially good candidates to treat bacterial diseases in humans.

After antibiotics were discovered, the phage approach was largely

abandoned in many parts of the world (particularly English-speaking
countries). However, phages continued to be used for medical purposes
in a number of countries, including Russia, Georgia, and Poland, where
they remain in use today^{12,13}12,13start superscript, 12, comma, 13,
end superscript.

There is increasing interest in bringing back the "phage approach"

elsewhere, as antibiotic-resistant bacteria become more and more of a
problem. Research is still needed to see how safe and effective phages
are, but who knows? One day, your doctor might write you a prescription
for phages instead of penicillin!
ľypes of Baííieís
ľhe fouí types of baííieís aíe:

Physical baííieí
ľhese include the skin, body haií, cilia, eyelashes, the íespiíatoíy tíact, and the gastíointestinal tíact. ľhese
foím the fiíst line of defence.
ľhe skin does moíe than píoviding us with faií oí daík complexions. Ouí skin acts as a physical baííieí to the
entíy of pathogens. ľhe mucus coating in ouí nose and eaí is a píotective baííieí which tíaps the pathogen
befoíe it gets inside.

Physiological baííieís
We know that ouí stomach uses hydíochloíic acid to bíeak down the food molecules. Due to such astíongly
acidic enviíonment, most of the geíms that enteí ouí body along with the food aíe killed befoíe the fuítheí
píocess is caííied on.
Saliva in ouí mouth and teaís in ouí eyes also have the antibiotic píopeíty that does not allow thegíowth of
pathogens even though they aíe exposed all day.

Cellulaí baííieís
In spite of the physical and physiological baííieís, ceítain pathogens manage to enteí ouí body. ľhe cells
involved in this baííieí aíe leukocytes (WBC), neutíophils, lymphocytes, basophil, eosinophil, and monocytes.
All these cells aíe all píesent in the blood and tissues.

Cyīokine baííieís
ľhe cells in ouí body aíe smaíteí than we give them cíedit foí. Foí instance, in case a cell in ouí body
expeíiences a viíus invasion, it automatically secíetes píoteins called inteífeíons which foíms a coating aíound
the infected cell and píevents the cells aíound it fíom fuítheí infections.

Cells Involved In Innate Immunity

 Phagocytes: ľhese ciículate thíough the body and look foí any foíeign substance. ľhey engulf
and destíoy it defending the body against that pathogen.
 Macíophages: ľhese have the ability to move acíoss the walls of the ciículatoíy system. ľhey
íelease ceítain signals as cytokines to íecíuit otheí cells at the site of infections.
 Mast Cells: ľhese aíe impoítant foí healing wounds and defence against infections.
 Neutíophils: ľhese contain gíanules that aíe toxic in natuíe and kill any pathogen that comes
in contact.
 Eosinophils: ľhese contain highly toxic píoteins that kill any bacteíia oí paíasite in contact.
 Basophils: ľhese attack multicellulaí paíasites. Like the mast cells, these íelease histamine.
 Natuíal Killeí Cells: ľhese stop the spíead of infections by destíoying the infected host cells.
 Dendíitic Cells: ľhese aíe located in the tissues that aíe the points foí initial infections. ľhese cells
sense the infection and send the message to the íest of the immune system by antigen píesentation.
 Keywords

Autotrophic – organisms which can make their own food

Photosynthesis – the process by which plants make food from carbon dioxide and water using
energy from the sun trapped using chlorophyll contained in the chloroplast .

Heterotrophic – Organisms which eat other organisms to get their food

ATP – Molecules that releases energy when the terminal phosphate bond is broken to form ADP
Redox – Linked oxidation/reduction reactions

Hydrogen acceptor – molecules that accept hydrogen in cellular reactions

Electron transport chain – Series of carriers along which an electron is passed in a series of
redox

reactions resulting in the production of ATP

Grana – Stacks of thylakoid within a chloroplast

Thylakoid – membrane disc which is a unit of granum in a chloroplast
Stroma – matrix which surrounds the membrane stacks in a chloroplast
Photosystem I – Chlorophyll complex involved in cyclic and noncyclic photophosphorylation
Photosystem II – Chlorophyll complex involved in noncyclic photophosphorylation
Photochemical reaction- Reaction which depends on light
Photophosphorylation – Process by which ATP is made in plants whereby an excited electron
from PS I is passed along an electron transport chain to produce ATP and returned to PS I

Photolysis – The splitting of a water molecule by light

Calvin cycle – Series of reactions which make up the light independent stage of photosynthesis

resulting in the synthesis of carbohydrates from carbon dioxide

RuBP – 5 carbon compound found in the calvin cycle

RUBISCO – Enzyme involved in the removal of a molecule of CO2 from RuBP

GP – Phosphorylated 3 carbon compound in the Krebs cycle

GALP – Reduced form of GP also part of the Krebs cycle

Ecosystem – Environment including all the living organisms interacting, the cycling of nutrients
And the physical and chemical environment in which the organisms are living

Habitat – Place where an organism lives

Population – Group of organisms of the same species living and breeding together in a
particular niche in a habitat Commented [M1]:
Community – All of the population of living organisms which live in a habitat at any one time

Ecological niche - The role of an organism within an ecological community

Habitat niche – The role of an organism in relation to a specific habitat

Abiotic factors - nonliving elements of the ecosystem

Biotic factors – The living elements of a habitat the affect an organisms ability to survive
there.

Biosphere – all areas of the earth’s surface where living organisms survive

Biomes – Major ecosystems of the world

Succession – Process by which communities of organisms colonising an area change over time

Opportunist/ Pioneer Species – Organisms which are the first to colonise bare rock or sand

Humus – organic component of soil

Climax community – A self sustaining community with relatively constant biodiversity and
Species range. The most productive group of organisms that a given environment can support
long term

Plagioclimax – a climax community brought about by human intervention

Microclimate – small areas with a distinct climate which is different to the surrounding areas

Leaching - Loss of minerals from soil as water passes through rapidly

Loam – ideal soil with a wide range of particle sizes and plenty of humus

Intraspecific competition – Competition between members of the same species for the same
resources within a community

Interspecific competition – Competition between members of different species for the same
resources within a community

Endemic – found in a particular region or country

Biomass – Mass of biological material in a given organism or habitat

GPP – percentage of the energy from the sun which is transferred into plant material
NPP – percentage of the sun’s energy converted into plant biomass
Food Chain – Simple feeding interactions between organisms in a community
Trophic level - Feeding positions in a food chain or web
Food web – more complex food interaction between organisms in a community

Decomposers – An organism which breaks down dead plant and animal matter

Secondary production – Energy used to make new animal biomass

Carbon sinks - reservoirs where carbon is removed from the atmosphere and locked up in
organic material or inorganic compounds

Greenhouse effect – The way in which greenhouse gases reduce the amount of heat lost from
the

surface of the earth

Temperature proxies – Indirect or inferred measurements of the temperature of the earth

Error lines – Indications of the range of error in a given measurement or inference

Mean values – The value obtained by dividing the sum of a set of values by the number of
values in the set

Interglacial – periods between ice ages

Wiggle matching – A process used to calibrate inferred, indirect, or imprecise way of
measuring.

Calibration – checking adjusting or standardising a piece of measuring equipment

Correlation – A factor that appears to be linked to a change or event.
Causal relationship – one factor directly causes an effect in another

Extrapolate – Use available data on which to base estimations of value which fall outside the
known range

Optimum temperature – Temperature at which enzymes work best

Denature – When the tertiary and quaternary structure of the protein is destroyed
Biofuels – Fuels produced from biomass
Genome – All the DNA of an individual
Proteome – All the proteins produced from the DNA of an individual
Allele frequency – The relative frequency of a particular allele in a population
Gene families – A group of closely related genes
Sickle cell disease – A genetic disease affecting the formation of haemoglobin, which in turn
affects the shape of the red blood cells

DNA profiling - using a sample of DNA to identify an individual.

Rigor mortis – the stiffening of the muscles which takes place within a few hours of death as
the cells

run out of ATP

Forensic Entomology - The study of insect life in relation to crime

Envelope – a lipid outer layer found in some viruses
Capsid – protein coat of virus
Capsomeres – Repeating protein units which make up the capsid

Bacteriophages – viruses which infect bacteria

Reverse transcriptase – enzyme used by viruses to produce DNA molecules which correspond
to the viral genome
Plasmid – extra circular strand of DNA, separate from the main chromosome found in bacteria
Lysogenic Pathway – Stage in viral lifecycle when the viral DNA is inserted into the host DNA
so it is replicated everytime the host cell reproduces. The virus is dormant – it does not cause
disease

Non virulent – not disease causing

Provirus – Viral DNA inserted into the DNA of the host cell so that it is replicated everytime the
host cell replicates

Lytic pathway – Stage in viral lifecycle when the viral DNA is replicated is replicated
independently of the host cell DNA and the virus is virulent

Virulent – capable of causing disease

Retrovirus – Viruses with RNA as their genetic material and relatively complex lifecycles
Exocytosis – moving substances out of a cell by emptying a membrane bound vesicle
Hypertonic – a solution with a higher solute concentration than the cell contents
Mesosome – infolding of the cell membrane seen in some bacteria
Capsule – Layer of starch, gelatin, protein or glycolipid which protects bacteria from
phagocytosis by

white blood cells. This is a slime layer if it is very thin

Pilli – Thread like protein projections from the surface of some bacteria which seem to be used
for attachment to the host cell and for sexual reproduction

Flagella – Thin extension made up of many stranded helix of the protein flagelin which makes
about 100 revolutions per second and moves the bacterium along

Peptidoglycan – Parallel polysaccharide chains with short peptide cross-linkages found in

bacterial cell walls

Gram staining – one way of identifying different types of bacteria

Gram positive – Bacteria which stain purply-blue with gram staining

Teichoic acid – chemical found in the walls of gram positive bacteria which binds to the crystal
violet colour in the gram stain to give the typical gram positive colour

Gram negative – Bacteria which stain red with gram staining

Cocci – spherical bacteria often linked together in chains
Bacilli – Rod shaped bacteria
Spirilla – Bacteria with a twisted shape
Vibrio’s – comma shaped bacteria
Obligate aerobes – organisms which cannot survive without oxygen for cellular respiration

Facultative anaerobes – organisms which use oxygen for cellular respiration if it is available
but can manage without it

Obligate anaerobe – organism which cannot survive with oxygen for cellular respiration
Generation time – Time between divisions of bacteria

Conjugation – method by which bacteria exchange genetic information

Sex pilus – strand of cytoplasm between to bacteria during sexual reproduction

Endotoxins – lipopolysaccharides which are part of the outer layer of gram negative bacteria
which cause symptoms of disease

Exotoxins – soluble proteins produced and released into the body by bacteria which often cause
severe symptoms of disease

Sebum – oily substance produced by the skin which contains chemicals which inhibit the growth
of

microorganisms

Lysozymes – enzymes found in mucus and tears which are capable of destroying microbial
cell walls.

Part of the nonspecific defence system

Biopsies – A sample of tissue removed from the body to be examined for signs of disease
Antigens – unique markers on the surface of every cell
Inflammation – nonspecific response to infection which involved the release of histamines,
raising of temperature locally, dilation of blood vessels and swelling

Mast cells – Cells found in many tissues as part of the immune response. They secrete
histamins

Histamines – chemical released in both inflammatory and allergic responses

Phagocytosis – The process by which phagocytes engulf and digest bacteria or other
pathogens

Granulocytes – White blood cells which have granules that can be stained in their cytoplasm

Phagocyte – General term to describe white blood cells which engulf and digest pathogens

Interferons – proteins that inhibit viral replication within cells

B cells – A type of lymphocyte involved in the specific immune response

Immunoglobins – membrane bound antibodies

T cells – Cells of the immune system made in the white bone marrow but activated in the
thymus

gland

T killer cells – T cells of the immune system which bind to infected cells and interact with the
cell

membrane to destroy the infected cell and pathogens with it

T helper cells – T cells of the immune system which produce cytokines in the specific immune
response

MHCs – proteins which display antigens on the surface of cells

T memory cells – cloned cells which remain in the body and rapidly become active if the same
antigen is encountered again

B effector cells – precursors of plasma cell clones which produce antibodies

B memory cells – very long lived cells which allow the body to respond rapidly to the second
invasion by a particular pathogen

Clonal selection- cloning of B-cells which are producing the right antibody to bind to and
destroy a particular pathogen

Plasma cell – part of the immune response

Antibody – protein produced in response to the presence of a specific antigen on the surface of
a foreign cell

Subjective evidence – Evidence about a disease based on how an individual feels

Selective toxicity – chemicals which interfere with the metabolism or functioning of a
pathogen with minimal damage to the human host
Bacteriostatic – A chemical which stops bacteria from growing
Bactericidal – A chemical which kills bacteria
Broad spectrum antibiotics – kills or inhibits a wide range of different bacteria

Narrow spectrum antibiotics – Targets one or two specific pathogens

MRSA – Bacterium which is resistant to most commonly used antibiotics

Natural active immunity – The immunity which results from natural infection of the body
and the

production of antibodies by the immune system

Natural passive immunity – Immunity resulting from antibodies passing naturally from a
mother to

her baby through the placenta

Immunisation – the process of protecting people from infection by giving them artificial
Vaccination – the procedure by which you immunise people to produce immunity to disease
Artificial passive immunity – immunity which results when antibodies formed in one
individual are extracted and injected into another individual

Herd immunity – The benefit to society of large cohorts of the population being vaccinated
against a particular disease. Herd immunity means that the weakest members who cannot be or
are not vaccinated for any reason are protected by the fact that everyone else is immune to the
disease so there is no pool of infection in the community
Important diagrams
Ecological Sampling

We need ecological sampling to measure the following:

› Abundance:
The number of organisms of a certain species in a certain area.
› Distribution:
Where is a species located within a certain area.
› Density:
Number of organisms per unit area. To calculate density: count the
total number of a certain species found and divide by the area of
quadrats. (organism/unit area)
› Frequency:
Percentage occurrence of a certain organism in a certain habitat. To
calculate frequency, count the number of quadrats having the
organism and divide by the total number of quadrats placed.

› Percentage cover: Percentage of the ground covered by an

organism.
It may be calculated using a frame (grid) quadrat, to count one of
the squares it must be more than half-full.

Types of Sampling
› Random Sampling:
Use random numbers to generate points and collect data from
quadrats.
› Systematic sampling:
Place quadrats at regular intervals.
N.B. Only go for systematic sampling if there is a clear pattern of
transition or a clear indication of a non uniform habitat (rocky shore
for example).

Steps of Random Sampling:

1. Choose an area of the field as a sample.
2. Take samples at random points from the selected area using a
computer model to generate the random points.
3. Use a suitable technique a. Plants: Quadrats (0.25 m2 quadrats
placed at the generated random points) b. Animals: Other methods
4. Apply the suitable equation. (density, percentage cover or
frequency)
5. Repeat to ensure reliability. 6. Take the average of your results
and multiply by the whole field area.

Tools of Sampling for Plants

› Frame quadrats: for both random and systematic sampling.
› Point quadrats: for both random and systematic sampling.
› Transects: for systematic sampling only.

Frame Quadrat
› Could be either a subdivided frame
or a simple square quadrat.
› Suitable for terrestrial habitats.
› The most common one is the 0.25
m2 quadrat.

N.B.
● Quadrats are usually divided into smaller sections (25 smaller
squares for example) why? This makes counting organisms easier
and more precise. Also estimating the percentage cover is easier
as each square represents 4%.
● It is difficult to estimate the effect of an abiotic factor (light
intensity for example) on the distribution of a certain plant
species, because there are other factors affecting distribution
such as temperature. Moreover, there is no data available on
other factors to estimate their effect.

Point (pin) Quadrat

› Linear frame through which knitting needles are
dropped to hit the vegetations studied.
› Every time the pin hits a vegetation is recorded a
“hit”. And every time it fails is recorded as a “miss”

Transects
A Transect is a line along which samples are taken in a linear pattern.
It is more suitable for nonuniform habitats such as rocky shores.
1. Line Transects:
A tape measure is placed along the transect and organisms touching
the tape are recorded.
2. Belt Transects:
Data is collected along the
transect using frame quadrats
placed next to each other.
3. Interrupted Transects:
Instead of investigating the whole
transect, you can take
measurements at regular intervals
using point quadrats.

Tools of Sampling for Animals

› MRR = Mark, Release and Recapture method.
1. Capture the 1st sample of animals using an appropriate method “see
methods next page”.
2. Mark the captured animal using a non-toxic paint.

3. Release the marked animals.

4. After an appropriate time interval, capture another sample and
count them. Split the animals found “marked” in the second sample
and record their number.
5. Use the Lincoln index to calculate the population size.
S = population size.
S1 = Total number of 1st sample “marked”.
S2 = Total number of 2nd sample.
S3 = Number found to be marked in 2nd sample.

› Precautions:
1. Use non-toxic paint that doesn’t come off.
2. Mark hidden sites not to attract predators.
3. Use the same method of capture and leave for a suitable time.

› Assumptions:
1. No births or deaths occurred.
2. No migration in or out.
3. No increase or decrease in predation.
4. Marks didn’t come off.

Evaluation of Sampling Process

› Experimental limitations
● Constant change of abiotic conditions.
● Organisms are continuously moving.
● Sampling is taken within a small time.

● Only 1 study is not enough to build a conclusion.

› Safety issues
● Risk of exposure to the wild or fields such as insect bites.

› Ethical issues
● Ethical concerns about the safety of living organisms.
● Disruption of normal habitat.

Remember: Measuring the 2 Aspects of Biodiversity

› Species Richness:
Total number of different species in a certain area measured by
random sampling → 10 Quadrats are randomly placed in an area, all
the species found in quadrats are recorded and used to estimate
species richness.
The different genes with all their different alleles within each
species are measured by genetic analysis = Number of genes x
Number of alleles in a certain species
Biodiversity = species richness * genetic diversity