Edexcel International alevelbiology.co.

uk
Advanced Level
Biology

Unit 4: Energy, Environment,

Microbiology and Immunity

SPECIFICATION

Topic 5: Energy Flow, Ecosystems and the Environment

This topic builds an appreciation that photosynthesis is the primary process that
underpins the majority of ecosystems, and provides students with an understanding of
how ecosystems work. The topic continues by looking at whether climate change will
lead to extinction of species or evolution by natural selection, and looks at the evidence
for global warming and its effects on plants and animals. By the end of the topic
students should appreciate how scientific understanding can make us aware of our
responsibilities as stewards of the environment.

Topic 6: Microbiology, Immunity and Forensics

This topic starts by looking at how forensic pathologists use a wide variety of analytical
techniques to determine the identity of a person or other animal, and to establish the
time and cause of death of an organism, including humans. It then considers how
bacteria and viruses use a variety of routes into their hosts and how hosts have evolved
barriers and internal mechanisms to combat infections. These protections are not
always successful and many people in the world still die from infectious diseases. This
topic also investigates the evolutionary battles that take place between invading
pathogens and their hosts.
Edexcel International alevelbiology.co.uk
Advanced Level
Biology

Topic 5: Energy Flow,

Ecosystems and the
Environment
SPECIFICATION
• 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
• Understand how photophosphorylation of ADP requires energy and that hydrolysis of ATP
provides an immediate supply of energy for biological processes
• 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
• 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)
• 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)
• Understand the structure of chloroplasts in relation to their role in photosynthesis
• Understand what is meant by the terms absorption spectrum and action spectrum
• Understand that chloroplast pigments can be separated using chromatography and the
pigments identified using Rf values
• Understand the relationship between gross primary productivity (GPP), net primary
productivity (NPP) and plant respiration (R). Be able to calculate net primary productivity
• Know how to calculate the efficiency of biomass and energy transfers between trophic
levels
Edexcel International alevelbiology.co.uk
Advanced Level
Biology

Topic 5: Energy Flow,

Ecosystems and the
Environment
SPECIFICATION
• Understand what is meant by the terms population, community, habitat and ecosystem
• Understand that the numbers and distribution of organisms in a habitat are controlled by
biotic and abiotic factors
• Understand how the concept of niche accounts for the distribution and abundance of
organisms in a habitat
• Understand the stages of succession from colonisation to the formation of a climax
community
• 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
• Understand the causes of anthropogenic climate change, including the role of
greenhouse gases in the greenhouse effect
• Understand how knowledge of the carbon cycle can be applied to methods to reduce
atmospheric levels of carbon dioxide
• Understand that data can be extrapolated to make predictions and that these are used in
models of future climate change
• Understand that models for climate change have limitations
• Understand the effects of climate change (changing rainfall patterns and changes in
seasonal cycles) on plants and animals (distribution of species, development and
lifecycles)
• Understand the effect of temperature on the rate of enzyme activity and its impact on
plants, animals and microorganisms, to include Q10
Edexcel International alevelbiology.co.uk
Advanced Level
Biology

Topic 5: Energy Flow,

Ecosystems and the
Environment
SPECIFICATION
• Understand how evolution (a change in allele frequency) can come about through gene
mutation and natural selection
• Understand how isolation reduces gene flow between populations, leading to allopatric or
sympatric speciation
• 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
• 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
The chloroplast structure in relation to photosynthesis:
A chloroplast is a double membrane-bound organelle of a plant cell.
In the inner membrane, sets of interconnected and stacked fluid-filled membrane sacs are
present that are known as thylakoids.
Thylakoids stack together to form the granum.
The fluid inside the inner membrane of a chloroplast, surrounding the granum, is called
thestroma.
A green-coloured pigment called chlorophyll is present inside the chloroplast.

The Structure of a Chloroplast

Image Source: OpenStax CNX

Overall reaction of photosynthesis

Light energy is absorbed by a chlorophyll molecule and is passed along a pathway to
other chlorophyll molecules.
The energy “excites” one of its electrons enough to leave the molecule and be
transferred to a nearby primary electron acceptor. A molecule of water splits to release
an electron, which is needed to replace the one donated. Oxygen and hydrogen ions are
formed from the splitting of water.
The hydrogen is stored into glucose by combining it with carbon dioxide and
releasing oxygen into the atmosphere.

Two stages of photosynthesis: Light dependent reaction and light independent reaction
Image Source: OpenStax CNX (middle)
The light-dependent reaction

1. Chlorophyll absorbs light, leading to photoionisation of chlorophyll.

▪ A chlorophyll molecule absorbs a photon of light.

▪ So, it moves from ground state to excited state.
▪ The chlorophyll pigments are arranged in light-harvesting complexes.
▪ Light-harvesting complexes are Photosystem I (PS I) and Photosystem II (PS II).
▪ Each system has one primary pigment molecule called reaction centre.
▪ Reaction centre starts the process.

2. Some of the energy from electrons released during photoionisation is conserved in the
production of ATP and reduced NADP.

▪ The added energy released during movement of chlorophyll to excited state lifts the
electrons to be used for reduction of NADP+.
▪ The excited state is unstable and the chlorophyll molecule regains its lost electron from
splitting a water molecule and coming back to ground state.
▪ During these processes, energy is utilised to convert ADP+ Pi to ATP.
▪ The above process is phosphorylation and, since it takes place in the presence of light, it
is called photophosphorylation.

Structures of PS II and PS I
Image Source: Openstax
The light-dependent reaction

3. (a) The production of ATP involves electron transfer associated with the transfer of
electrons down the electron transfer chain.

▪ As discussed earlier, PS I absorbs light at 700 nm and PSII at 680 nm. Therefore the
reaction centres are referred to as P700 and P680, respectively.
▪ The photophosphorylation that takes place to form ATP is of two types: Non-cyclic
photophosphorylation (involving P680 and P700) and cyclic photophosphorylation
involving only P700.
▪ Non-cyclic photophosphorylation: The electrons given out by P680 are moved to electron
carriers forming electron transport chain and causing oxidation-reduction reactions.
▪ ATP is produced during this, as discussed earlier, and the electron passed to P700.
▪ Again, electrons pass through electron carriers and finally form NADP to NADPH.
▪ At this stage, excess hydrogen ions are made available by photolysis of water, and PS II
regains lost electrons.
▪ The net result of non-cyclic photophosphorylation is oxygen, NADPH2 and ATP.
▪ Cyclic photophosphorylation: Electrons given up by P700 move through Electron
Transport Chain and finally back to P700.
▪ Formation of ATP is in the same way as that of non-cyclic photophosphorylation.

Non-cyclic Photophosphorylation and Cyclic Photophosphorylation

Image Source: OpenStax CNX
The light-dependent reaction

3. (b) Chemiosmotic theory.

▸ Photolysis of water molecule takes place on the inner side of the membrane.
▸ Protons produced by splitting of water accumulate within the lumen of the thylakoid.
▸ When electrons pass through PS, protons pass through the membrane.
▸ This is because primary acceptor of electrons is located towards the outer side of the
membrane.
▸ It transfers its electron to an H carrier instead of an electron carrier.
▸ So, this molecule removes a proton from stroma during transporting electron.
▸ When this molecule passes its electron to the inner side of the membrane, the proton is
also released with it in the lumen of the membrane.
▸ NADP reductase enzyme present on the stroma side of the membrane helps in the
reduction of NADP+ to NADP+H+ in the presence of protons.
▸ ATP synthase enzyme embedded in the membrane of chloroplast acts as the channel for
the passage of protons.
▸ It also catalyzes the formation of ATP.

ATP Synthesis through Chemiosmosis.

Image Source: OpenStax CNX

4. Photolysis of water produces protons, electrons and oxygen.

▸ Water is split into H+, [O] and electrons.

▸ Oxygen is one of the by-products of photosynthesis.
▸ Electrons lost from PS II regained from PS I.
▸ Water splitting complex is associated with PS II.
▸ 2H2O → 4H+ + O2 + 4e-
The fixation of carbon dioxide and the light-independent stages of photosynthesis.
1. The light-independent reaction uses reduced NADP from the light-dependent reaction to
form a simple sugar:
▸ Two molecules of NADPH is used for the reduction of 3- phosphoglycerate to triose
phosphate in the light-independent reaction.
▸ NADPH is produced in the light-dependent reaction.
2. The hydrolysis of ATP, also from the light-dependent reaction, provides the additional
energy for this reaction:
▸ Two molecules of ATP are also used for the reduction of 3- phosphoglycerate to triose
phosphate along with NADPH.
▸ One molecule of ATP is used in the regeneration of triose phosphate to ribulose 1,5-
bisphosphate.
▸ ATP is produced in the light-dependent reaction.
Steps in light-independent reaction.

1. Carbon dioxide reacts with ribulose bisphosphate (RuBP) to form two molecules of
glycerate 3-phosphate (GP). This reaction is catalysed by the enzyme rubisco.

RUBP + CO2 + RuBisCO → 3-PGA (CARBOXYLATION: 1st step of C3 cycle)

2. ATP and reduced NADP from the light-dependent reaction are used to reduce GP to
triose phosphate (glyceraldehyde phosphate).

3 PGA + ATP + NADPH →Triose Phosphate + ADP + NADP + + inorganic phosphate

(REDUCTION: 2nd step of C3 cycle)

3. Some of the triose phosphate (glyceraldehyde phosphate) is used to regenerate RuBP

in the Calvin cycle

Triose Phosphate + ATP → Ribulose 1,5- bisphosphate + ADP

(REGENERATION: 3rd step of C3 cycle)

4. Some of the triose phosphate (glyceraldehyde phosphate) is converted to useful

organic substances

Triose Phosphate → Sucrose, Starch

Overall Reaction of Calvin (C3) Cycle:
6RuBP + 6CO2 + 12H2O + 18ATP + 12NADPH →6RuBP + C6H12O6 + 18ADP + 12 NADP

C3 Cycle
Image Source: OpenStax CNX

The uses of Triose phosphate (glyceraldehyde phosphate) (TP/GALP).

The third and fourth steps of the light–independent reaction show the uses of triose
phosphate (glyceraldehyde phosphate) (TP/GALP).
1. Two triose phosphates join to form one glucose, and many glucose join to form starch.
2. Lipids are also synthesised from triose phosphate:
(a) Triose phosphate produces glycerol, and glycerate 3- phosphate produces fatty
acids.
(b) Glycerol and fatty acids join to form lipids.
Absorption and action spectra

The natural visible spectrum of light contains 7 different colours which can be perceived by
the human eye. Our retinal pigments can only “see” (absorb) wavelengths between 700 nm
and 400 nm of light, a spectrum that is therefore called visible light. Each of these 7 colours
has a wavelength associated with it. We can see the colour as that part of the light which has
not been absorbed (i.e. it has been reflected) by an object. So, the rest of the colours are
absorbed, major of which is the colour complimentary to which we can see.

Absorption spectrum refers to the graph of absorbance versus the wavelength.

An action spectrum is a graph of the rate of a physiological activity plotted against
wavelength of light.
Absorption spectra of different chlorophylls show a range of wavelengths for each pigment
and highlight the need for plants efficient at photosynthesis to have a combination of
pigments.

Photosynthetic Pigments

Plant chloroplasts contain chlorophyll pigments for light absorption as well as other
pigments. Chlorophylls can be either chlorophyll a or chlorophyll b which gives different
absorption peaks. Different pigments to absorb different wavelengths maximises the rate of
photosynthesis.
These pigments can be identified by running thin layer chromatography. Many photosynthetic
organisms have a mixture of pigments, and by using these pigments, the organism can
absorb energy from a wider range of wavelengths. Not all photosynthetic organisms have full
access to sunlight. Some organisms grow underwater where intensity and quality of light
decrease and change with depth. Other organisms grow in competition for light. Plants that
commonly grow in the shade have adapted to low levels of light by changing the relative
concentrations of their chlorophyll pigments.

Chromatographic separation of pigments (left) and Absorbance spectra of chlorophyll a & b (right)
Image Source: OpenStax CNX
Synthesis of organic compounds by plants
Solar energy is the fundamental source of energy for all the life on Earth. It is primarily
tapped by plants to produce organic molecules.

1) An ecosystem is defined as the set of all biotic (life forms) and abiotic (non-living)
environments in a specific area.
2) Every ecosystem contains producers— life forms that synthesise their own food through
photosynthesis. Plants and algae come under this category.
3) Plants use solar energy in the form of light, and the CO 2 from the atmosphere or dissolved
CO2 (aquatic plants) for photosynthesis to produce glucose and other sugars.
4) Plant respiration uses up a part of the sugars produced in photosynthesis.
5) The remaining glucose undergoes reactions for conversion into biological molecules like
cellulose and other complex organic molecules, which constitute the living material, i.e. plant
biomass.
6) Biomass is a measure of stored chemical energy.
7) The food chain is the thread of transfer of this energy. Primary consumers eat producers
and are themselves eaten by secondary consumers, who in turn are eaten by tertiary
consumers.

Photosynthesis
Image Source: OpenStax CNX
Biomass (dry) and energy are useful representations of ecosystem structure

The mass of living organism is its biomass, e.g. the mass of plant material, herbivores,
carnivores etc. Energy is stored in the form of biomass, and it is transferred through the
ecosystem between trophic levels. In a way, we can say the transfer of energy is the
same that of transfer of biomass. Therefore, transfer of biomass/energy through the
ecosystem occurs due to the presence of food chains and food web. A food chain is a
simple linear chain of different trophic levels where organism of one trophic level eats
organism of another trophic level.

The biomass should be dry mass (since water stores no energy) and is measured in kg
m-2. The biomass may be found by drying and weighing the organisms at each trophic
level, or by counting them and multiplying by an average individual mass. Pyramids of
biomass are usually pyramid-shaped (even if the pyramid of numbers isn’t), since if a
trophic level gains all its mass from the level below, then it cannot have more mass than
that level (you cannot weigh more than you eat).

Biomass can be measured in terms of the mass of carbon in an organism or the dry mass of
tissue per specified area. Calorimetry is used for estimation of the chemical energy stored in
dry biomass.

▸ Mass of the organism after water removal is called dry mass.

▸ The sample of an organism is dried in an oven at low temperature with regular monitoring
of the decrease in weight due to water loss. When the weight reaches a constant value, it
is taken to be the dry mass.
▸ If required, scaling of the result from the sample is done to get the biomass (dry mass) of
total population or region under observation. It is often measured in kg m -2.
▸ Half (50%) of the dry mass is usually accepted as the mass of carbon.
▸ Loss of leaves and barks typically leads to change of biomass of trees over a period of
time, often seasonally. Hence, a measurement of biomass over a time period is
necessary, and typically the units are kg m -2 yr-1.

Amount of chemical energy stored in biomass is measured in joules (J) or kilojoules (kJ).
The general method followed is:

1. Burning of a sample of dry biomass and the use of released energy to heat a known
volume of water.
2. Calculation of the chemical energy of the dry biomass from the change in temperature of
the water.
Biomass and energy transfers through ecosystems
Transfer of energy is the same that of transfer of biomass.
Therefore, transfer of biomass/energy through the ecosystem occurs due to the
presence of food chains and food web. The food chain is a simple linear chain of
different trophic levels where an organism of one trophic level eats organism of another
trophic level.
For example:
Producers (grasses)→ primary consumers (herbivores such as deer) → secondary
consumer (carnivore such as lion).

Food web is a network of multiple food chains. Due to this network, now it is no more
simple and linear, rather it has become complex and web-like.
For example, grass is eaten by grass hopper, grasshopper is eaten by frog and small
bird. Both of these are eaten by a snake. Snake and small bird are both eaten by hawk.
Mainly transfer of biomass/energy takes place from producers to consumers.
Typically, only around 10% of the biomass in each level is passed on to the next level.
Mass is lost at each stage of a food chain for two reasons:

• Some of the biomass absorbed by a consumer is used in respiration and is converted

to carbon dioxide and water, which are excreted (when organisms respire they lose
mass).

• Some of the biomass is simply not eaten by the consumers in the next trophic level, or
is ingested but then egested again without being absorbed. This unused biomass can
include plant cellulose cell walls, wood, bones, teeth, skin and hair.

Pyramids of energy are always pyramidal (energy can be lost but cannot be created),
and are always very shallow, since the transfer of energy from one trophic level to the
next is very inefficient Typically, only around 1% of the energy in each level is passed on
to the next level. The “missing” energy, which is not passed on to the next level, is lost
eventually as heat.

Transfer of energy
Image Source: Wikipedia
GPP and NPP as measures of chemical energy available in plant tissues

Total light energy converted into chemical energy per unit area per unit time by a plant is
known as Gross Primary Production (GPP).

Respiration of plants account for nearly 50% of the GPP lost to the environment as heat. This
is known as respiratory loss or plant respiration (R).

The energy remaining after respiratory loss is called Net Primary Production (NPP).

NPP is the energy available to the plants for their other biological functions like growth and
reproduction, and it is also available to primary consumers (like herbivores, fungi and
bacteria).
i.e. NPP = GPP – R

Efficiency of energy transfer and net production by consumers

All the consumers, be it primary, secondary or tertiary, store a part of the energy received
from the immediate previous trophic level in the food chain.

The reason for the loss of most of the chemical energy stored in the consumer’s food is due
to:

1. Incomplete ingestion of food– the roots, stems, bones, etc. are parts of the food of
various consumers that are generally not eaten.
2. Incomplete digestion of the food– the loss of indigestible materials as faeces.
3. Loss to the environment– this includes loss of a certain percentage of energy in the
form of respiration and urine.

After these losses are taken into account, the leftover energy is considered to be the net
production calculated using the formula:

N = I – (F + R)

Where,
I = Chemical energy stored in ingested food,
F = Chemical energy lost to the environment in faeces and urine,
R = The respiratory losses to the environment.

Primary and secondary productivity are the rates of primary or secondary production,
respectively, typically measured as biomass per unit area, per unit time (kJ ha –1year–1).
Efficiency of energy transfers between trophic levels
▸ Food chains are simple lines of energy transfer through trophic levels.
▸ Food webs are lines of interaction of organisms across various trophic levels.
▸ Decomposers are the final destination of all food chains and food webs.

A Food Chain (left) and a Food Web (right)

Image Source: OpenStax CNX

The measurement of energy transfer efficiency between two successive trophic levels is
termed the trophic level transfer efficiency (TLTE) and is defined by the formula:

Net production efficiency (NPE) allows ecologists to quantify how efficiently organisms of a
particular trophic level incorporate the energy they receive into biomass; it is calculated using
the following formula:

Where,
Net consumer productivity is the energy content available to the organisms of the next
trophic level.
Assimilation is the biomass (energy content generated per unit area) of the present trophic
level after accounting for the energy lost due to incomplete ingestion of food, energy used
for respiration, and energy lost as waste.
Distribution of organisms in a habitat
The maximum size of a population of one species an ecosystem can sustain, taking all
the available resources into account.
▸ The carrying capacity depends on:
• Abiotic factors, i.e. the available resources such as food, water and habitat.
• The amount of resources each individual consumes.
• Biotic factors like competition between organisms for the available resources.
Increased competition (both interspecific and intraspecific) reduces the carrying
capacity.
a) Interspecific = Competition between members of different species for the same
resources. Better-adapted species have a greater chance of survival.
b) Intraspecific = Competition amongst the members of the same species for the
same resources.
• Interactions, for instance predator-prey relationships, between two species.

Niche
▸ The niche of an organism is its role in the ecosystem. All the species have their
specific niche.
▸ It is difficult to completely describe the niche of an organism because there are
multiple ways in which it interacts with other components of the ecosystem.
▸ Both living and nonliving components of the ecosystem govern the niche occupied by
a species.
▸The niche plays a crucial role in the development of adaptive features.

Resources are often limited within a habitat and multiple species may compete to
obtain them. All species have an ecological niche in the ecosystem, which describes
how they acquire the resources they need and how they interact with other species in
the community. The competitive exclusion principle states that two species cannot
occupy the same niche in a habitat. In other words, different species cannot coexist in a
community if they are competing for all the same resources.
Effects of biotic and abiotic factors on population size

Populations
A population is the number of a particular species living in one habitat. Population Ecology is
concerned with the question: why is the population the size it is? This means understanding
the various factors that affect the population. Many different factors interact to determine
population size, and it can be very difficult to determine which factors are the most
important.

Factors can be split into two broad groups:

Abiotic factors
Abiotic factors are all the physical or non-living aspects to an ecosystem. These include:

• Climatic factors, such as temperature; water/humidity; light/shade; current (wind/water),

frost
• Edaphic (soil) factors, such as pH; mineral supply; soil texture; soil moisture
• Topographic factors, such as altitude, slope, aspect
• Human factors, such as pollution
• Catastrophes, such as floods and fire

Abiotic factors can vary within a habitat, giving microclimates in microhabitats, e.g. the
abiotic factors under a stone are very different from those on top of an adjacent stone wall.

Abiotic factors tend to be density independent factors, i.e. the size of the effect is
independent of the size of the population. For example, a low light intensity will limit plant
growth regardless of the number of plants present. Many abiotic factors vary with the
seasons, and this can cause a periodic oscillation in the population size.

Biotic factors
Biotic factors are all the living aspects of an ecosystem, i.e. food, competitors, predators,
parasites and pathogens.

Biotic factors tend to be density-dependent factors, i.e. the size of the effect depends on the
size of the population. For example, the competition will be greater the population.

Biotic factors such as availability and access to resources, can limit the population size of a
species.
Biotic Factors

Prey and predator relationship

○ When the population of prey increases, the population of predator also increases due to
an increase in their food.
○ Now due to an increase in the population of a predator, the population of prey will
decrease (negative feedback).
○ Finally, due to a decrease in the population of prey, there will be decrease in the
population of predator (again negative feedback), and thus the cycle starts again.

Prey-predator relationship
Image Source: OpenStax CNX

Interspecific competition
▸ Competition between organisms of different species for the same resources.
▸ Availability of resources is limited to both populations.
▸ Both the populations can get insufficient energy for growth and reproduction. As a result,
the population sizes of both populations will be lower.
▸ This type of competition also affects species distribution.
▸ For example, out of two competing species, one is well adapted to its environment, and
another is less adapted. Therefore, during the course of time, the less adapted one will
out-competed and will not be able to exist.

Intraspecific competition:
▸ Competition between organisms of the same species for same resources.
▸ When resources are plenty, the population of a species increases.
▸ Now with the increase in the population, more organisms will compete for availability of
space and food in the same region.
▸ Gradually, food and space will become limited or insufficient for all the organisms
present in that particular area and therefore, population starts to decrease.
▸ As population becomes smaller, there will be less competition for space and food.
▸ This situation gives a better chance for growth and reproduction and population begins to
increase again.
Ecosystems are not stagnant. They continuously evolve and change.

Succession to a climax community

▸ The process of ecosystem change is called succession. It may be primary or secondary.
▸ All the species living in the ecosystem induce changes, which may make living conditions
favourable for other species, in some cases, and adverse in others.
▸ Primary succession occurs on land that is initially bare, with no soil or any other organic
material. This land may appear as a result of a volcanic eruption or recession of sea level.
▸ Secondary succession occurs on land that has soil cover but has become devoid of
vegetation. This may happen as a result of a natural disaster, forest fire or deforestation by
humans.

Primary Succession
▸ Seeds and spores blown by wind arrive on the bare land.
▸ The first species to colonise the barren area are known as pioneer species. These are
specially adapted to bear the harsh conditions and grow where other forms of life cannot
survive.
▸ The pioneer species alter the environment. When they die, microorganisms decompose the
dead organic matter to form basic soil.
▸ The basic soil helps retain water, allowing a greater number of species to grow in the
region.
▸ As more and more species grow, and then decompose after dying, the soil becomes richer
in minerals. This allows for a number of diverse species to grow. Larger plants can now
grow in the deep and mineral-rich soil.
▸ Newer species may make conditions less favourable for the pioneer species, which slowly
perish.
▸ Diverse and large plants provide a habitat for lots of animal species.
▸ Over time, the ecosystem becomes complex as the diversity of species increases.

Secondary Succession
▸ Progresses in almost the same way as primary succession. As the soil layer is already
present, succession starts at a later stage and the pioneer species are usually the larger
plants.
▸ At each stage, the ecosystem is constantly changing. New species keep colonising the
ecosystem. Better adapted species out-compete the plants and animals that are already
present.
▸ The final stage is called the climax community. This is when the ecosystem is already
supporting the most complex and well-adapted forms of life. This is a certain steady stage.
▸ Different climates have different climax communities, as abiotic factors are different.
Global Warming is causing Climate change on the Earth

Causes of Global Warming

▸ Excessive use of fossil fuels: Burning fossil fuels release carbon dioxide in the atmosphere
which is a greenhouse gas & increases the temperatures on earth.
▸Deforestation: Cutting down of trees in massive numbers has led to the inability of utilising
the carbon dioxide in the atmosphere.
▸Farming: Use of pesticides, fertilisers etcs give a huge boost to plantation crops, which are
cut after their season, leaving behinds tons & tons of CO 2 in the atmosphere. Livestock
animals release huge amounts of another greenhouse gas called methane.
▸Waste mismanagement: Millions of tons of plastic & other wastes are dumped every year
which release methane & other toxic greenhouse gases.
▸Mining: This industry takes about 5% of global transport and adversely affects the
atmosphere by burning fossil fuels. Moreover, it also produces coal – a highly inefficient
fossil fuel which is a major contributor to global warming

Effects of Global Warming

▸Disrupts normal ecosystems, habitats and plant reproduction.
▸Disrupts the life cycle of migratory birds and animals.
▸Melts glaciers and polar ice, leading to floods and imbalanced rainfall.
▸Acidification of the oceans because of absorbing a large amount of CO 2.
▸Affect human health and population due to floods, droughts etc.
▸Excessive droughts and heatwaves.
▸Certain insects are adapted to warmer climates but, if there is a global temperature rise,
these insects can survive in new regions and bring new pathogens that can impact
ecosystems with species that cannot fight the new diseases.
▸Impacts the nature of pollen, and the gradual increase in the type of pollen that thrives
better in a warmer climate shows a trend of increasing temperature.
▸Melting of polar ice caps reduces reflection of solar energy back into space, reduces
species biodiversity, destroys habitats and some species become extinct.
▸Rising sea levels from melting ice caps and thermal expansion of oceans could flood low-
lying lands, reducing terrestrial habitats and reducing freshwater habitats as seawater
moves up rivers.
Understanding the carbon cycle for reducing atmospheric levels of carbon dioxide
All carbon-based organisms require carbon for building macromolecules. For that purpose,
the carbon cycle, like the nitrogen cycle, exists. But the difference is that, unlike
atmospheric nitrogen, atmospheric CO2 can be directly utilised by plants without any
conversion.

Carbon Cycle
Image Source: OpenStax CNX

▸ The cycle includes metabolic and ecological processes such as photosynthesis,

respiration and decomposition, and physical processes like combustion and weathering
of rocks.
▸ Participants in the carbon cycle are roughly divided among producers, consumers, and
decomposers of organic carbon compounds.
▸ Human activity releases carbon dioxide and methane, two of the most significant
greenhouse gases, into the atmosphere. The primary mechanism that releases carbon
dioxide is the burning of fossil fuels, such as gasoline, coal, and natural gas.
▸ Recent studies show that the abrupt increase in levels of CO 2 due to heavy
industrialisation has occurred after the 1950s, a trend which has never occurred before.
▸ Cutting down of trees and deforestation by fire impacts the level of CO 2 adversely.
▸ Reforestation and use of biofuels for our energy consumption needs is the way forward
for a sustainable environment.
Effect of temperature on enzyme activity
● High temperatures cause denaturation due to the breaking of bonds holding the tertiary
structure together (H bonds/disulphide bridges/ionic bonds).
● The active site is altered (changes shape), substrates cannot bind, and no enzyme
substrate complexes form.
● Inability to form enzyme substrate complexes impairs the fruit-bearing capacity of the
plants & trees, leading to decrease in population.
● Enzyme inactivity in microbes leads to their inability to decompose the waste and
hinders the natural cycles.
● Enzyme inactivity in animals leads to various effects like diseases, genetic changes,
decrease in fertility rates etc.

Effect of temperature on enzyme activity

Image Source: Wikimedia Commons

Evidence for Global Warming

Scientists cannot go back in time to directly measure
climatic variables, such as average temperature and
precipitation, rather they must indirectly measure
temperature.
Antarctic ice cores have been collected and analysed
to indirectly estimate the temperature of the Earth over
the past 400,000 years.
By measuring the amount of CO2 trapped in the ice,
scientists have determined past atmospheric CO 2
concentrations.
The atmospheric concentration of CO2 has risen
steadily since the beginning of industrialisation.
The effect of global warming can be seen in the
continuing retreat of glaciers.

Correlation between carbon dioxide concentration

and global temperature
Image Source: OpenStax CNX
Evidence for Global Warming
Dendrochronology (tree rings) is a method to ascertain the rise in temperature of Earth.
It is the study of the rings formed within tree trunks.
Typically, a new ring is formed within the trunk each year.
The number of rings can be used to determine the age of the tree.

Dendrochronology
Image Source: Wikimedia Commons

Recent studies show that the thickness of the rings formed in the 20th century is greater than
those formed earlier.
This is a clear indication of a warmer climate.

Pollen in peat bogs is another method for determining climate change.

Pollen is often trapped in peat bogs - a type of acidic wetland, which preserves the pollen
layer-by-layer as time passes.
Collecting pollen gives insight into the climate that was prevalent when the pollen was
trapped.
Climate change impacts the nature of pollen, and the gradual increase in the type of pollen
that thrives better in a warmer climate shows a trend of increasing temperature.

Peat bog
Image Source: Wikimedia Commons
Global warming due to human activity – models for prediction of future global
warming
Human activity releases carbon dioxide and methane, two of the most significant greenhouse
gases, into the atmosphere. The primary mechanism that releases carbon dioxide is the
burning of fossil fuels, such as gasoline, coal, and natural gas.

Abrupt increase in the levels of CO2 due to heavy industrialisation

Image Source: Wikimedia Commons

Recent studies show that the abrupt increase in levels of CO 2 due to heavy industrialisation
has occurred after the 1950s, a trend which has never occurred before.

Predictions based on the present levels of global warming due to emissions provide a few
scenarios:
 If the emissions continue to increase at a rapid rate, most of the Earth will become
unsuitable for many life forms.
 The second possibility is that, if the emissions continue to be same, there will still be
some scope to limit it to a tolerable level.
The best scenario is that we take measures to reduce the emission of greenhouse gases to
bring the global temperature down eventually.

Climate change - historic and predicted

Scientific conclusions about controversial issues on actions to reduce global warming

• Global warming as an issue proven by science is beyond any doubt.

• Economics being the leading factor in the world today, science more often takes a back
seat.
• Policymakers are often not from a science background, nor do they take the scientific
reports seriously.
• Political and economic decisions often supersede the climate change concerns.
• Huge corporation in the traditional energy sector influence the decisions taken by
policymakers.
• Global warming concerns are often sidelined in favour of mining and oil companies and
electricity production from burning extremely low-efficiency fuels like coal, due to
economic benefits.

Burning of Amazon rainforest in Brazil

Image Source: Wikimedia Commons

A prime example of negligence and reluctance to work on global warming, while promoting
the mining and farming companies, is the massive fire in the Brazilian rainforest Amazon. The
reluctance of the Brazilian government in putting out the fire has drawn international criticism
since Amazon accounts for 20% of the total forest cover on earth. This is a classic example
of how actions that should be taken to reduce global warming or the degree to which humans
are affecting global warming can sometimes depend on who is reaching the conclusions.
Evolution (a change in the allele frequency) can come about through gene mutation
and natural selection.
The Hardy-Weinberg principle states that the frequency of alleles and genotypes in a
population will remain constant from one generation to the next generation in the absence of
evolutionary influences.
▸ The formula for calculating allele frequency is: p+q=1, where p = frequency of dominant
allele and q = frequency of recessive allele.
▸ The formula for calculating genotype frequency is: p²+2pq+q²=1, where p²= frequency of
the dominant genotype, 2pq= frequency of the heterozygous genotype and q²= frequency
of the recessive genotype.
Natural selection
Natural selection increases the frequency of alleles conferring advantage and decreases the
frequency of alleles conferring a disadvantage. Disease, predation and competition for
means of survival are the factors that usually dictate natural selection. Due to natural
selection, individuals with a selective advantage survive and thrive while the numbers of
those with a disadvantage dwindle.

Mutation
New alleles are formed. Changes due to mutations also occur independently within the two
populations (sympatric speciation). Reproductive isolation may be the result of mutations
(allopatric speciation).

Reproductive isolation leads to speciation

● Development of a new species (speciation) is the result of reproductive isolation
(when a population of the same species fails to breed successfully).
● Reproductive isolation occurs due to changes in alleles and phenotypes as a result of
geographical isolation (physical barriers), which divides a population, e.g. floods,
earthquakes, etc.
● The different populations become genetically distinct on either side of the barrier due
to differing environmental conditions and, over a long time, become separate species
that cannot breed with one another.

Reproductive isolation
Image Source: OpenStax CNX
Sustainability of resources depends on effective management of the conflict between
human needs and conservation

Sustainability of resources depends on effective management of the conflict between human

needs and conservation, as illustrated by attempts to conserve fish stocks and reduce
possible causes of climate change.

Preserving fish stocks This can be achieved by fisheries management which involves fishing
regulations that hinder overfishing of particular species and cooperation between fisheries as
regards fishing seasons and times to enable fish stocks to be replenished. Fishermen should
also be regulated as to what type of nets they can use for fishing to minimize unintended
capture of marine organisms. Consumers should also choose sustainably sources fish. Fish
breeding programmes are another way of maintaining fish stocks and replenishing depleting
fish stocks.

Fish farming in Vietnam (top) and Mexico (bottom)

Image Source: Wikimedia Commons
Sustainability of resources depends on effective management of the conflict between
human needs and conservation

Sustainability of resources depends on effective management of the conflict between human

needs and conservation, as illustrated by attempts to conserve fish stocks and reduce
possible causes of climate change.

Reducing possible causes of climate change This can be done in the following ways:

1. High pricing on carbon– Increasing the price of carbon-containing petrochemicals based

materials will incentivize the investment on renewable and non-toxic alternatives.
2. Removing fossil-fuel subsidies– This will help redistributing the money for the poor as
well as reducing indiscriminate wastage of fuels like going off for unnecessary rides and
short-distance drives. It will also increase the use of public transport that will help with
traffic as well as economical means of transport.
3. Support energy efficiency– Methods should be developed to use energy for industrial
purposes with minimum environmental impact. Use of solar and wind energy should be
promoted.
4. Climate-smart agriculture– Reducing the usage of herbicides, pesticides, and
insecticides as well as chemical fertilizers.
5. Careful city-planning– Planning cities well to reduce wastes and build zones with enough
tree cover inside the cities.

Role of the scientific journals, the peer review process and scientific conferences in
validating evidence related to the debate about climate change

Global warming and climate change as an issue proven by science are beyond any doubt.
A lot of scientific data is available from high-tech instruments used by scientists to prove the
real concerns of climate change.
Most of the scientific studies clearly and overwhelmingly support serious concern due to
climate change.

However, political and economic decisions often supersede the climate change concerns.
Huge corporation in the traditional energy sector influence the decisions taken by
policymakers.
In this scenario, the authentic data published by scientists through peer review and
organizing conferences helps in creating awareness among the citizens which can pave the
way for the policymakers to rethink on the policies regarding climate change.
Edexcel International alevelbiology.co.uk
Advanced Level
Biology

Topic 6: Microbiology, Immunity

and Forensics

SPECIFICATION
• Understand the principles and techniques involved in culturing microorganisms, using
aseptic technique
• Understand the different methods of measuring the growth of microorganisms, as
illustrated by cell counts, dilution plating, mass and optical methods (turbidity)
• 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
• 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)
• Understand what is meant by the terms lytic and latency
• Understand how Mycobacterium tuberculosis and human immunodeficiency virus (HIV)
infect human cells, causing symptoms that may result in death
• Know the major routes pathogens may take when entering the body
• Understand the role of barriers in protecting the body from infection, including skin,
stomach acid, and gut and skin flora
• Understand the non-specific responses of the body to infection, including inflammation,
lysozyme action, interferon and phagocytosis
• Understand the roles of antigens and antibodies in the body’s immune response including
the involvement of plasma cells, macrophages and antigen-presenting cells
• 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
• Understand how individuals may develop immunity (natural, artificial, active and passive)
• Understand how the theory of an ‘evolutionary race’ between pathogens and their hosts is
supported by evasion mechanisms shown by pathogens
Edexcel International alevelbiology.co.uk
Advanced Level
Biology

Topic 6: Microbiology, Immunity

and Forensics

SPECIFICATION

• Understand the difference between bacteriostatic and bactericidal antibiotics

• 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
• Know the role of microorganisms in the decomposition of organic matter and the
recycling of carbon
• Know how DNA can be amplified using the polymerase chain reaction (PCR)
• Know how gel electrophoresis can be used to separate DNA fragments of different length
• Understand how DNA profiling is used for identification and determining genetic
relationships between organisms (plants and animals)
• Understand how to determine the time of death of a mammal by examining the extent of
decomposition, stage of succession, forensic entomology, body temperature and degree
of muscle contraction
Aseptic techniques used in culturing organisms
Successful cell culture depends heavily on keeping the cells free from contamination by
microorganisms such as bacteria, fungi, and viruses. Nonsterile supplies, media, and
reagents, airborne particles laden with microorganisms, unclean incubators, and dirty work
surfaces are all sources of biological contamination.

Aseptic technique that are designed to provide a barrier between the microorganisms in the
environment and the sterile cell culture, depends upon a set of procedures to reduce the
probability of contamination from these sources. The elements of aseptic technique are a
sterile work area, good personal hygiene, sterile reagents and media, and sterile handling.

Principles and techniques involved in culturing microorganisms

There are 5 basic techniques for culturing microbes –

1. Inoculation– Introduction of an inoculum (small sample) of the microbes into the
medium containing nutrients for their growth.
2. Incubation– Providing the ambient surroundings, including temperature and light (or its
absence) for the microbes to grow. The visible growth is called culture & may take hours,
or even weeks to appear depending on the microbe.
3. Isolation– Separation of the macroscopic lumps (in solid media) or turbid floating
masses (in liquid media) of colonies of microbes. Then a small part of it is taken and
spread uniformly in a separate medium so that it contains only one species of microbes.
This is called sub-culturing.
4. Inspection– Macroscopic observation for determining growth features like texture,
colour and size of the colonies. Use of staining techniques to quickly inspect the
morphology.
5. Identification – Exact classification of the microbes based on microscopic, chemical and
genetic analysis. This step is fundamental to verifying the previous steps as well as
determining the microbes being cultured.

Microbe culture should follow the principles of a sterile environment, clean equipment,
adequate pH for microbial growth and the appropriate media.

Phosphate solubilizing bacteria cultured in petri dish

Use of different Culture media (Growth media)

Bacteria will grow on practically any source of organic food which provides carbon
compounds to be respired for energy, and nitrogen compounds to be incorporated into
proteins for growth. These substances are normally provided dissolved in water.
However, in nature, bacteria can break down solid and insoluble substances by releasing
enzymes into the substrate in which they are growing. These substances are thus
broken down or digested to simpler substances, and the process is called extracellular
digestion because it takes place outside the bacterial cells.

The two media used normally in bacteriology are: a clear soup-like liquid nutrient broth,
usually in tubes, and nutrient agar, which is set into a jelly by the addition of a seaweed
extract called agar, and when melted poured into glass or plastic Petri dishes, also
known as "plates".

A standard carbon source is the glucose, and nitrogen is often provided by peptones
(partially digested proteins), or inorganic salts. Minerals and vitamins may also be
provided, according to the growth requirements of the bacteria. Combinations of
chemicals (buffers) may be used to keep the pH stable. Measured amounts of the
concentrates are added to water and dissolved to reconstitute the media.

Sometimes, substances are mixed into media, in order to suppress the growth of other
types of bacteria. There are many such selective media.

Examples of selective media include:

● Eosin methylene blue contains dyes that are toxic for Gram-positive bacteria.
● YM (yeast extract, malt extract agar) has a low pH, deterring bacterial growth.
● MacConkey agar is for Gram-negative bacteria.
● Hektoen enteric agar is selective for Gram-negative bacteria.

Four types of agar plate demonstrating differential

growth depending on bacterial metabolism
Image Source: Wikipedia
Measurement of Bacterial growth

Cell counts
Directly observing the bacteria under a microscope and counting their number. However,
this technique poses difficulties like the distinction of dead cells and an inability to
correctly identify cells in too-much diluted media.
Viable counts– Counting of only those cells that are capable of producing offspring by
division. This is also called plate count or colony count.

Dilution plating
A solution of bacteria at an unknown concentration is often serially diluted in order to
obtain at least one plate with a countable number of bacteria i.e., cell density in the
range of 30 to 300 colony units per plate. The counting method omits small colonies.

Counts of cells obtained via cultivation are orders of magnitude lower than those
directly observed via microscope. This is because microbiologists are able to cultivate
only 1% of microbes using current techniques.

Mass and optical methods (turbidity)

Each cell scatters light as it passes through the cell. Using a spectrophotometer. The
unscattered light can be directly correlated to the number of cells. Scattering is directly
proportional to the cell count, and the optical density is not linearly related with cell
count with the increase in cell density as the cells re-scatter the already scattered light.

Counts of cells obtained via cultivation and direct sampling

Image Source: Wikipedia
Phases of a bacterial growth curve

Four different phases of bacterial growth are lag phase (A), log phase or exponential
phase (B), stationary phase (C), and death phase (D).

Lag phase (A): This is a phase of adaptation for bacteria. These are not able to divide
and are still adapting to the growth media. Synthesis of bacterial RNA, enzymes and
other molecules occurs during this phase.

Log phase or exponential phase (B): Bacteria multiply in terms of exponentials, i.e.
multiples of multiples and this rapid multiplication continue till the nutrients are
available.

Stationary phase (C): This stage comes when the nutrients dwindle, or inhibiting
byproducts like organic acids are formed due to the bacterial life process. Genetic
mutation can arise in this phase.

Death phase (D): The bacteria die out during this phase due to lack of nutrients and/or
increase in temperature or imbalance in other environmental factors.

Phases of a bacterial growth curve

Image Source: Wikipedia
Structure of bacteria and viruses

Structure of Bacteria:
● Single-celled.
● The cell wall is made up of glycoproteins.
● An outer membrane called a plasma membrane is present.
● Are very small in micrometres.
● Have cytoplasm and cell organelles, including ribosomes.
● DNA is freely floating inside the cytoplasm, it doesn’t reside inside the nucleus.
● Bacterial cells have hair-like structures known as pili (small) and flagellum (long).

Virus structure:
● Are smaller than bacteria.
● Plasma membrane, cytoplasm and ribosome are absent in a virus.
● The nucleic acid is either DNA or RNA.
● The outer membrane is called a capsid.
● Some viruses also have an outer layer called an envelope that is formed from the cell
membrane of a previous host cell.

Structure of bacteria Virus structure

Source: Openstax
AQA A-Level Biology 3.2.1.2 Structure of prokaryotic cells and of viruses

Various types of viruses:

λ (lambda) phage (DNA)

Lambda phage consists of a virus particle including a head
(also known as a capsid), a tail and tail fibers.
Enterobacteria phage λ (lambda phage, coliphage λ) is a
bacterial virus, or bacteriophage, that infects the bacterial
species Escherichia coli. This virus is temperate and may
reside within the genome of its host through lysogeny.
Schematic model of Tobacco mosaic virus.
1. nucleic acid
2. capsomer (protomer)
3. capsid

Ebola (RNA) virus

It has a cylindrical structure with an encoded
glycoprotein.
It contains negative-sense and unsegmented
single-stranded RNA that is linear.

HIV
Single-stranded (+)sense RNA with DNA
intermediate in life-cycle (Retroviruses).
Genome is (+)sense but unique among
viruses in that it is DIPLOID and does not
serve as mRNA, but as a template for
reverse transcription.
Bacterial and viral infectious diseases have a sequence of symptoms that may result in
death
Infectious pathologies are typically transmittable infections because of their potentiality
of transmission from one person or from one species to another.

Tuberculosis – caused by Mycobacterium tuberculosis (TB)

It starts with a primary infection in the lungs and quickly spreads to the lymph nodes,
bones and gut.
It spreads via aerosol droplets and unpasteurised milk and is particularly prevalent in
overcrowded areas.
People suffering malnutrition are more susceptible.

Symptoms
Coughing up blood, shortness of breath, fever, chest pain and sweating.

AIDS – caused by Human Immunodeficiency Virus (HIV)

Acquired Immune Deficiency Syndrome (AIDS), is a syndrome caused by the retrovirus
Human Immunodeficiency Virus (HIV).
HIV pathogens infect and destroy the T helper cells of the immune system, and without
these the immune system does not respond adequately to infection.
When T-Cell numbers are low, the body is particularly vulnerable to infection by anything
from the common cold to tuberculosis.
Thus, AIDS is not a disease.
HIV is the virus that causes AIDS, which is a syndrome. Affects the CD4 receptor cells.
It spreads via exchange of body fluids (sexual intercourse, intravenous needle sharing,
blood transfusions).

Symptoms
HIV has a few weeks to incubate, but AIDs may not develop for up to ten years.
HIV - fever and then none.
AIDs - hugely increased susceptibility to disease, such as pneumonia and TB.
Non-specific responses of the body to infection

Inflammation
● After a foreign antigen enters the body, the site of infection becomes red, swollen and
painful. This reaction is called inflammation.
● After the pathogen enters the body, different immunomodulatory molecules are
produced.
● This triggers the widening and increased permeability of the blood vessels.
● Increased blood flow brings immune cells to the site of infection.
● Immune cells enter the infected tissues and kill the pathogens.

Interferons
● They are antiviral proteins that prevent virus infection in healthy cells.
● The mechanism of action of interferon involves inhibiting viral replication.
● They activate cells of the specific immune responses against the virus.
● They promote inflammation to the site of infection.

Phagocytosis and lysozyme

● Phagocytosis is carried out by phagocytes.
● Phagocytes are also called antigen-presenting cells (APCs).
● They are the first line of defence against a pathogen.
● The mechanism of action of phagocytes are as follows:
● It recognises the pathogen and engulfs it, forming a phagocytic vacuole.
● Lysozymes containing various digestive enzymes then fuse with the phagocytic vacuole.
● Enzymes present in the lysozyme break the pathogen into smaller antigens.
● These small antigens then stick on the surface of the phagocytic cells and are
presented to the T or B cells.

Phagocytosis and lysozyme

Source: CNX.org
Activation of T cells by macrophages
● T cells have receptors present on the cell surface.
● These receptors bind with the complementary antigens present on the surface of
macrophages (a type of antigen-presenting cell).
● This binding activates the T cells.
● Activated T cells carry out different functions, such as:
 T helper cells secrete substances that activate the B cells.
 T killer cells kill the pathogen-infected cells.
 T memory cells are responsible for the secondary immune response.

T cell activation (source CNX.org)

B cell activation and plasma cells

● A B cell is a type of white blood cell and is activated by T helper cells.
● They are covered with antibodies.
● Upon recognition of an antigen, they form antigen-antibody complexes by binding with a
complementary antigen.
● Every B cell binds with the specific antigen.
● Plasma cells are clones of B cells.
● They secrete antibodies specific for a particular antigen.
● Antibodies clear infections by:
a. Agglutination reactions
b. Neutralising the toxins secreted by the pathogens and
c. Preventing the pathogen from binding with uninfected host cells.

T cell-dependent B cell activation (source: http://cnx.org)

Roles of B cells and T cells

● T helper cells help activate the B cells by secreting different substances.

● T killer cells kill the pathogen-infected cells by attaching themselves to it.
● T memory cells are produced after being exposed to any antigens. They remain in the
circulation after the pathogen is destroyed. If the same pathogen enters the body again,
these memory T cells get activated and cause a secondary immune response.
● Effector B cells are responsible for producing antibody-antigen complexes and help
clear infection by agglutination reactions, neutralising toxins, and preventing the
pathogen from infecting a host cell.
● Memory B cells are produced in a similar way to memory T cell and produce plasma
cells.

Development of individual immunity

Natural immunity:
When an individual gets exposed to a live pathogen,
They develop a primary immune response and the memory cells remain in the
circulation
Their acquired immunity is natural and is known as natural immunity.
Artificial immunity:
When immunity occurs because of vaccination, that type of immunity is called artificial
immunity.
Active immunity:
When the body’s immune system starts making antibodies after being exposed to an
antigen, the immunity is called active immunity. For example, when vaccinated, the body
is exposed to a harmless dose of an antigen so that the immune system starts
producing antibodies against the antigen.
Passive immunity:
In this type of immunity, antibodies made by another organism are given to boost the
immune system of another. For example, in natural passive immunity, a baby gets its
primary immunity through the antibodies it receives from its mother milk.
Evolutionary race between pathogens and their hosts

● The immune system of vertebrates has evolved over millions of years. Pathogens have
also have devised mechanisms to evade the immune system of the host cells.
● This struggle between vertebrate hosts and the pathogen is known as the evolutionary
race.
● As a result, pathogens have developed some evasion mechanisms.

Human Immunodeficiency Virus kills the host’s T cells, thereby reducing the number of
effective immune cells in the body.
It also mutates the genes responsible for producing antigenic proteins by a process
known as antigenic variation. This helps the viral proteins evade recognition by memory
cells. So, every time, the host’s immune system has to produce a different primary
response for a new strain of HIV.
HIV disrupts the antigen presentation by APCs.

Mycobacterium Tuberculosis also has some evasion mechanisms

Inside the lung’s phagocytic cells M. tuberculosis prevents the lysozyme from fusing
with phagocytic vacuoles. Killing of the bacterium by the phagocytosis is thereby
prevented.
This bacterium also prevents antigen presentation by APCs, preventing killing by
phagocytosis.

Antibiotics
Chemicals that kill or prevent the growth of bacteria are called antibiotics.
They are drugs that are used as a treatment for bacterial infection.

There are two types of antibiotics that are used for preventing bacterial infection:

1. Bactericidal: This type of antibiotic kills bacteria directly. They inhibit the enzymes
involved in bacterial cell wall formation. This weakening of the cell wall causes water to
move inside the cell leading to cell death.
2. Bacteriostatic: This type of antibiotic slows down the growth of the bacteria either by
preventing protein synthesis or DNA replication or any other cellular metabolism of the
bacterium.
Hospital-acquired infections (HAI)
● Hospital-acquired infections (HAI) are infections which are acquired in a hospital and, in
most cases, transmitted by poor hygiene practices by hospital staff and visitors.
● The patients have a weakened immune system so they are prone to the infection.
Certain codes of practice, if implemented, can prevent this HAI. They are as follows:
● Wash hands before and after visiting patients. This rule is applicable for hospital
staff as well as visitors.
● Disinfecting hospital beds and surfaces more frequently
● Moving HAI patients to an isolation ward specific for such infections.
Some HAIs are caused by antibiotic-resistant bacteria.
This type of infection is difficult to treat as very few or, and in some cases, no antibiotics will
work.
For this type of infection, a code of conduct has been generated in order to prevent the
bacteria from becoming further antibiotic resistant.

The rules are as follows:

● Doctors shouldn’t prescribe antibiotics for minor bacterial infections or viral

infections.
● Prevent doctors from prescribing antibiotics for minor infections and for viral
infections.
● Antibiotics shouldn’t be prescribed for preventing infections.
● Prescribe narrow-spectrum antibiotics that are specific for a particular bacterium,
if possible.
● Rotate the antibiotic prescribed.
● Patients should adhere to the treatment regimen that they have been prescribed.
They should also complete the full course of the antibiotic prescribed by the
doctor so that no infection is left behind, which can develop resistance.
Role of microorganisms in the decomposition of organic matter and the recycling of
carbon
Decomposition has 2 components:
1. Autolysis– the destruction of the body cells by own enzymes.
2. Putrefaction– microorganisms (like fungi and bacteria) decompose the body by
feeding on it.

Microbes breakdown the body and consume the fats, carbohydrates, nucleic acids etc.
from therein.
This energy promotes further respiration and reproduction leading to further growth in
the number of microbes and which, in turn, leads to further decomposition.
This process also multiplies the release of carbon into the biosphere through respiration
of these microbes and hence completes the carbon cycle.

Major routes through which pathogens enter the body

● Cut skin
● The digestive system via contaminated food
● Through the respiratory system
● Other mucosal surfaces such as through the genitals, nose, or mouth.

Role of barriers in protecting the body from infection

Human skin comprises of three layers - Epidermis, Dermis, Subcutis (Hypodermis).
● The epidermis provides a dry, watertight barrier with sloughing dead cells
(keratinocytes).
● The dermis produces sweat and sebum, maintaining acidic pH that prevents most
bacteria from growing.
● The dermis also contains additional molecules that attack invading pathogen by a
process known as “phagocytosis” (e.g. neutrophils, macrophages, etc.).
● Commensal microorganisms present on the skin (skin flora) secrete fatty acids that
inhibit colonisation by other microbes.
Stomach acid
The acidic environment of the stomach kills most of the pathogens that enter through the
digestive system.
The gut
The gut or intestine contains harmless microorganisms (called flora) that compete with
the pathogen for nutrition and space. This activity restricts the pathogen from infecting
the body.
PCR - Polymerase chain reaction

PCR or a polymerase chain reaction amplifies DNA and make millions of copies of specific
regions in a very short amount of time.
The procedure of PCR is as follows:
● Setting up the reaction mixture containing the primer, the DNA sample to be amplified,
free nucleotides, and the DNA polymerase enzyme.
● The sample is heated to 95°C and cooled to 55°C to facilitate the binding of the DNA
primers with the DNA strand.
● The temperature is set to 72°C for DNA polymerase to work.
● DNA polymerase makes strands of new DNA by complement strand synthesis.
● Each cycle doubles the amount of DNA present in the sample, and this process repeats.

Polymerase chain reaction

Image source: Openstax
 6.10 Post-transcriptional modifications

Gel Electrophoresis:

• The gel electrophoresis is the separation of nucleic acids or chromosomes by using an

electric field.
• One end of the gel electrophoresis device has a slot near the negatively charged gel. The
negatively charged nucleic acids are placed in the slot.
• The other end of the gel-containing device has a positively charged electrode.
• When the electric field starts, the negatively charged nucleic acids, chromosome
fragments, or chromosomes move towards the positive electrode due to the attraction of
opposite charges. The smaller molecules move faster and reach closer to the other end
while the larger molecules travel less distance. So, this also helps in comparison to the
sizes of the fragments.
• Fluorescent dies can be used to see these fragments as bands on the gel

Image source: Openstax

Credit- James Jacob, Tompkins Cortland Community
College and International Rice Research Institute

DNA profiling

● DNA profiling can be used to determine the genetic correlation between two organisms,
either animal or plants.
● It is the genetic fingerprint of an organism’s DNA.
● This technique is based on the principle that everyone has different DNA so DNA
profiling will be different for everyone.
● In closely related organisms, the DNA profile will be similar.
● A greater number of DNA bands on the electrophoresis gel will be matched for closely
related species.
Forensics for determination of the time of death of a mammal
It is often important for police and forensic experts to establish a body’s time of death (TOD).
The information regarding TOD can be achieved by looking at several factors together. There
are a total of five factors that are important for this:
a. Body temperature:
● The human body produces heat from metabolic reactions like respiration.
● After death, body temperature starts falling due to the metabolism stopping.
● The human body cools at a rate of around 1.5°C to 2.0°C per hour.
● Different conditions affect the cooling rate such as clothing, air temperature, and body
weight.
b. Muscle contraction
● Rigor mortis (stiffening of the muscle) sets in around 4-6 hours after death.
● This occurs due to lack of oxygen supply to the muscles and lactic acid production due to
anaerobic metabolism.
● Due to increased lactic acid production, pH of the muscle becomes lower.
● The bonds between actin and myosin become fixed due to the absence of ATP, leading to
rigor mortis.
c. Forensic entomology
● After death, different microorganisms start colonising the body.
● Identification of the type of insects present in and on the body helps to establish TOD.
● Identifying the life cycle stages of the insects (e.g. presence of blowfly eggs or larvae)
also helps to estimate time of death.
d. Extent of decomposition
● Forensic scientists can use the extent of decomposition by microorganisms to establish
the time of death. For example, cells and tissue are broken down by the body’s own
microorganisms in the first few hours to a few days after TOD.
● Temperature and oxygen availability also affect tissue decomposition by microorganisms.
e. Stages of succession
● The changing types of organisms found on a dead body also help to identify TOD.
● Immediately after death, bacteria invade the body.
● As the body decomposes, flies start colonising the body and then beetles enter.
● Beetles decompose dry tissue and complete the decomposition of the body leaving behind
only the skeleton.
● This is affected by the location of the body such as above ground or in water etc.