Module 4: Biodiversity, evolution and disease

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Module 4: Biodiversity, evolution and disease

SPECIFICATION

4.1 Communicable diseases, disease prevention and the immune system

4.1.1 Communicable diseases, disease prevention and the immune system.

Learners should be able to demonstrate and apply their knowledge and understanding of:

(a) The different types of pathogen that can cause communicable diseases in plants and animals.

(b) The means of transmission of animal and plant communicable pathogens.

(c) Plant defences against pathogens.

(d) The primary non-specific defences against pathogens in animals.

(e) i) The structure and mode of action of phagocytes.

ii) Examination and drawing of cells observed in blood smears.

(f) The structure, different roles and modes of action of B and T lymphocytes in the specific immune response.(g) The primary and secondary immune responses.(h) The structure and general functions of antibodies.(i) An outline of the action of opsonins, agglutinins and anti-toxins.(j) The differences between active and passive immunity, and between natural and artificialimmunity.(k) Autoimmune diseases.

(l) The principles of vaccination and the role of vaccination programmes in the prevention ofepidemics.(m) Possible sources of medicines.(n) The benefits and risks of using antibiotics to manage bacterial infection.4.2 Biodiversity4.2.1 Biodiversity.(a) How biodiversity may be considered at different levels.(b) (i) How sampling is used in measuring the biodiversity of a habitat and the importanceof sampling.(ii) Practical investigations collecting random and non-random samples in the field.(c) How to measure species richness and species evenness in a habitat.(d) The use and interpretation of Simpson’s Index of Diversity (D) to calculate the biodiversity of a habitat.(e) How genetic biodiversity may be assessed, including calculations.(f) The factors affecting biodiversity.(g) The ecological, economic and aesthetic reasons for maintaining biodiversity.(h) In situ and ex situ methods of maintaining biodiversity.(i) International and local conservation agreements made to protect species and habitats.

4.2.2 Classification and evolution.

(a) The biological classification of species.

(b) The binomial system of naming species and the advantage of such a system.

(c) i) The features used to classify organisms into the five kingdoms: Prokaryotae, Protoctista, Fungi, Plantae, Animalia.

ii) The evidence that has led to new classification systems, such as the three domains of life, which clarifies relationships.

(d) The relationship between classification and phylogeny.

(e) The evidence for the theory of evolution by natural selection.

(f) The different types of variation.

(g) The different types of adaptations of organisms to their environment.

(h) The mechanism by which natural selection can affect the characteristics of a population over time.

(i) How evolution in some species has implications for human populations.

OCR A-Level Biology Module 4: Biodiversity, evolution and disease

Communicable diseases, disease prevention and the immune system

The disease that can be spread between the two organisms is called communicable disease and the organism that causes the disease is called pathogen such as bacteria, viruses, fungi etc.

Different types of pathogen that can cause communicable diseases in plants and animals

Bacterial Diseases

● Ring rot disease of plants affects potatoes and tomatoes.● Tuberculosis disease affects animals(humans and cattle).● Bacterial meningitis disease affects the humans.

Viral Diseases

● Tobacco mosaic disease affects the plants.● HIV/AIDS disease affects the humans.

Protoctista Diseases

● Potato/tomato late blight disease affects plants (potatoes/tomatoes).● Malaria caused by protoctist affects animals including humans.

Fungal Diseases

● Black sigatoka disease affects the banana plants.● Ringworm disease affects cattle.● Athlete’s foot disease affects humans.

Means of transmission of animal and plant communicable pathogens

● When disease is transmitted directly from one organism to another, it is called direct transmission.


● When disease is transmitted indirectly from one organism to another via an intermediate (air, water, food or another organism called vector), it is called indirect transmission.

Living conditions, climate and social factors also affect disease transmission:

● Overcrowded living conditions can increase the spread of many infectious diseases e.g.The risk of TB infection increased when lots of people live crowded together in a small place.This is because bacteria can remain in air for long periods and can infect new people.

● Climate can also increase the spread of many infectious diseases. E.g. During wet summers, potato/tomato late blight is more common because spores need water to spread.

● Social factors can also increase the spread of many infectious diseases e.g. the risk of HIV infection is high in areas where the people are less aware of the knowledge about disease transmission and there is no good healthcare.

Plant defence against pathogens

Physical defences

● Waxy cuticle over the plant stem and leaf provides a physical barrier against the pathogen entry. It also helps to reduce the risk of infection between plants as it doesn’t allow water to stay on the leaf.

● Cell wall also act as a physical barrier for the pathogens that make it past the waxy cuticle.

● During pathogen infection callose (polysaccharide) gets deposited between the plant cell wall and the plasma membrane that make it difficult for the pathogen to enter the cell.


Chemical defences by secretion of chemicals

● Plants secrete toxins which kills the insects reducing the risk of infection by plant viruses carried by them.

● Saponins are chemicals produced by some plants to destroy the cell membrane of pathogens.

Animal defences (primary, non-specific) against pathogens

Skin● Blocks the entry of pathogen.● Produce chemicals which can inhibit the growth of pathogens by lowering the pH.

Blood clotting● Prevents pathogen entry and blood loss by plugging the wound.

Wound repair : ● Outer layer of skin cells divide and migrate to the edges of the wound.● Tissue below the wound having collagen fibres contracts to bring the edges of wound

close together and wound is repaired leaving a scar.Inflammation ● Occurs as a result of tissue damage.● Include swelling, pain, heat and redness of the affected area due to release of

molecules from the damaged tissue, which helps in isolation of any pathogen and also brings WBCs to the area.

Expulsive reflexes ● Sneezing and coughing as a result of irritation of membrane of nostril and respiratory

tract are an attempt to expel the foreign substances automatically. Mucous membrane ● Protect body openings such as mouth, nostril, ears etc.● Mucus (sticky substance) secreted by some membranes trap the pathogens.

Structure and mode of action of phagocytes

● Non-specific immune response is carried by phagocytes (macrophage and neutrophils) by a process called phagocytosis.

● Phagocytes recognise the foreign antigen on pathogen and engulf them by extending pseudopodia around them.

● Pathogen contained in a vesicle called phagosome fuses with a lysosome, which contains hydrolytic enzymes to digest the contents of the the phagosome.

● Phagocyte act as antigen presenting cell (APC) by displaying the antigen on its surface to activate other cells of immune system.


Phagocytosis by macrophage Source : cnx.org

Neutrophils also act as phagocytes that respond to pathogen inside the body. Cytokines released by the cells at the site of wound, signals the neutrophil to move toward a wound and start phagocytosis.

Examination and drawing of cells observed in blood smears

● Blood smear is a sample of blood smeared over a microscopic slide.● Stains are added to the sample to make different cells visualise.● Example below shows how a blood smear look like:


Structure, Role and Mode of action of T and B lymphocytes (Types of WBC’s)

T Lymphocyte

● Surface of each T lymphocyte is covered by different receptors, which bind to a complementary antigen presented by APCs.

● T lymphocyte gets activated on binding to an antigen (clonal selection).● Then clonal expansion occurs in which T lymphocyte divides to produce clones that

differentiates into following types of T lymphocytes: T helper cells: release substances to activate B lymphocytes. T killer cells: attach to antigen on a pathogen and kill the cell. T regulatory cells: helps to stop immune system cells attacking the host’s body cells. Memory cells: remember the specific antigen and will recognise it in second time round.

B Lymphocyte

● Surface of each B lymphocyte (type of WBC) is covered by proteins called antibodies of different shapes, which bind to a complementary antigen to form antigen antibody complex.

● B lymphocyte gets activated on binding to an antigen together with the substances released from T helper cells (clonal selection).

● Then clonal expansion occurs in which B lymphocyte divides to produce plasma cells and memory cells.

● Plasma cells secrete lot of antibodies specific to the antigen.● Memory cells record the specific antibodies needed to bind the antigen in a second

time of pathogen attack.

Cell signalling helps to activate other WBCs that are needed for immune response. E.g. T helper cells are signalling to the B lymphocytes that there’s pathogen by releasing interleukin that bind to B cell receptors.

Primary and Secondary immune response● A primary immune response refers to the response brought about by a newly

encountered antigen.This response is very slow.● During this response plasma memory cells are produced by both T and B lymphocytes.

Memory cells do not function in the primary immune response but remain in body for a longer period.

● However if the same antigen enters again, the memory cells (both B and T memory cells) will proliferate and differentiate into antibody producing cells as the first line of defence in a secondary immune response.This response is very fast.


General structure and function of antibody

● Antibodies are Y-shaped and composed of two heavy and two light polypeptide chains.● Variable region: Forms antigen binding site that varies for each antigen.● Constant region: Allow binding to the receptors on the cells like phagocytes.

Structure of antibody Source: cnx.org (modified)

Functions of antibody

● Opsonins are molecules in the blood that attach to foreign antigens to aid phagocytosis.

● Antibodies can bind to two pathogens at same time resulting in clumping of pathogens. Phagocytes then engulf lot of pathogens bind to antibody at same time.This is called agglutination.

● Toxins produced by pathogens are neutralised by the anti-toxins (i.e. antibodies ) preventing the human cells from the effect of toxins.


Difference between active and passive immunity

Autoimmune diseases

● When immune system treats self antigens as foreign antigens and produce immune response against the organism’s own tissues.This condition is called as autoimmune diseases.

● E.g. Lupus is caused when immune system attacks cells of connective tissues resulting in painful inflammation of tissues. It also affects skin, joints, heart and lungs. Rheumatoid arthritis is caused when immune system attacks cells in joints resulting in pain and inflammation.


Principles of vaccination and the role of vaccination programmes● A vaccine contains noninfectious antigens associated with a specific disease.● A vaccine will cause a small primary immune response with the purpose of production

of memory cells.● Thus the person will gain immunity against that specific disease providing an

immediate effective secondary response as if those antigens are encountered again.● Examples of routine vaccines:

MMR vaccine protect against measles, mumps and rubella. Meningitis C vaccine protect against the bacteria that cause meningitis C.● Vaccine and vaccination programme changes:

E.g. The influenza vaccine has been changed every year because the antigen on influenza virus changes regularly resulting in failure of memory cells (produced by vaccination with one strain) to recognise other strains.● Effectiveness of new vaccines are tested by WHO (World Health Organisation) and

CDC(Centre for Disease Control).● Programme of vaccination is then implemented by government for the most suitable

vaccine.

Possible sources of medicines and personalised medicines

● Many Plants, animals and microorganisms produce compound which are the source of medicines (e.g. Penicillin is obtained from fungus). So it is necessary to protect biodiversity.

● Personalised medicines are medicines tailored to an individual’s DNA.They are more effective as they are developed according to someone’s genetic makeup and their responsiveness to drugs.

● Artificial proteins, cells, microorganisms and medicines are designed using technology. This is called synthetic biology.

Benefits and risks to use antibiotics

● Antibiotics are widely used to treat bacterial infections as a result death rate decreased but there are risk to use them as they can cause allergic reactions in some people.

● Another risk is development of antibiotic resistance in bacteria due to genetic mutations due to which it become difficult to treat some life threatening bacterial infections. E.g. MRSA (causes serious wound infections) is resistant to several antibiotics like methicillin.


Biodiversity

The variety of living organisms living in area is known as biodiversity.Levels of biodiversity● Habitat diversity: number of different habitats in an area. E.g. Sand dunes, woodland,

streams etc.● Species diversity: number different species (species richness) and abundance of each

species (species evenness) in an area. E.g. Many species of plants, insects, birds etc. may be present in a woodland.

● Genetic diversity: variation of alleles within a species. E.g. Different breeds of cow are the result of variation of alleles within cow species.

Measurement of biodiversity by sampling● Types of sampling: random sampling and non-random sampling.

For random sampling, sample should be random to avoid any bias in your results. For non-random sampling three types of non random samples are there: Systematic: Samples are taken at fixed intervals. Opportunistic: Sample are chosen by the investigator. Stratified: When different areas in a habitat are sampled separately in proportion to their part of habitat as a whole.

Measuring species richness and species evenness● Species richness is measured by random sampling of habitat and then by counting

the number of different species. Higher the number of species, greater the species richness.

● Species evenness is measured by random sampling of a habitat and counting the number of individuals of each different species. E.g.


Index of diversity (D)● Another way of measuring biodiversity is to study index of diversity.● Index of diversity called simpson’s index of diversity can be calculated by an equation

that takes into account species richness as well as species evenness.

Calculation of an index of diversity (D):

D = 1 - ( ∑( n/N)2 )

N = Total number of organisms of all species

n = Total number of organisms of one species

Σ = Summation

Greater the value of ‘D’, greater is the diversity. The value of ‘D’ will be 1 if all individuals belong to same species.

Assessment of genetic diversity

● It is very important to calculate the genetic diversity of a population because in an isolated populations like zoo genetic diversity is very low due to which population will not be able to adapt itself and wiped out.

● Therefore calculations of genetic diversity helps to increase the genetic diversity of the population if needed, e.g. breeding programmes in zoos.

● Genetic diversity can be measured by finding out the proportion of polymorphic gene loci in an organism.

Proportion of polymorphic gene loci = number of polymorphic gene loci/ total number of loci

Factors affecting biodiversity

● Human population growth decreases biodiversity.● Habitat diversity is decreased due to human development.● Genetic and species diversity is decreased due to over-exploitation of resources to

meet the requirements of growing population.


● Genetic diversity decreased as a result of urbanisation which isolate species and they are unable to interbreed.

● Increased use of monoculture (growing of single variety of a single crop) decline biodiversity because habitats are lost to make a way for large fields.

● A climate change can increase or decrease the biodiversity, e.g. migration (due to climate change) decreases biodiversity in the area the species migrate from, and increase biodiversity in the areas they migrate.

Reasons for maintaining biodiversity

Ecological reasons● Organisms in an ecosystem are interdependent for food ,shelter etc.therefore

loss of one species may affect the other.● Loss of keystone species (some species on which many of other species depend)

would change the ecosystem dramatically.● Genetic resources (crops,plants used for medicines) should be protected as they

provide everyday products like drugs, fuel, clothing etc.

Economic reasons● Continuous monoculture causes soil depletion because nutrients required by the

crop are gradually used up.This results in increased spending on fertilisers.

Aesthetic reasons● Biodiversity brings joy to millions of people as it is rich in attractive landscapes.

In situ and ex situ conservation

● Protecting species in their natural habitat is called in situ or on site conservation.● National parks, wildlife reserves, marine conservation zones have been

established in which human activity is restricted or controlled.● Protecting a species by removing part of population from natural habitat and

placing it in a new location is called ex situ or off site conservation.● Botanical gardens (where variety of rare and endangered plants are grown) and

seed banks (seeds are frozen to make them available for future when natural sources are not available) are established to conserve biodiversity.

● Relocating an organism to safer area and captivity breeding (in the zoo) are other ways to protect animals.


International and local agreements to conserve biodiversity

Rio Convention on Biological diversity (CBD)● It aims to develop strategies to use animals and plant resources in a sustainable way.

CITES Agreement (Convention on International Trade in Endangered Species)● According to this agreement it is illegal to trade in products made from endangered

species and it also limits the trade by licensing.The countryside stewardship scheme (CSS) in UK (local agreement)● Its aim was to promote specific management techniques to landowners which help to

improve and extend wildlife habitats.

4.2.2 Classification and evolution

Biological classification of species ● It is very difficult to study the large number of organisms one by one. Therefore,

grouping of organisms have been done based on similarities and differences between the organisms (classification).● Naming of organisms and organising them into group is the

work of taxonomy. Each group is called taxon (plural taxa).● The organisms are classified using eight levels of group which

are Domain, Kingdom, Phylum, Class, Order, Family, Genus and Species.● These taxa are arranged in a hierarchy without any overlapping.

The largest taxa is placed at the top and smallest at the bottom.● After that organisms are placed into different taxa serially

according to their fundamental characteristics representing that particular taxa and also according to similarities and dissimilarities with other organisms. ● The most similar organisms are present in species taxa and

most dissimilar in domain taxa.

Hierarchy of classification Source : cnx.org


● Then as per their characteristic features they are placed into either of the five kingdoms: Monera, Protoctista, Fungi, Plantae and Animalia.

The Binomial Nomenclature (naming system) was given by Carolus von Linnaeus in 1753.

● This nomenclature is binomial because it has two parts.● The first part represents genus and starts with capital letter. The second part

represents species and starts with small letter.● The names should be written in italics while typing and underlined while writing.

Example: Scientific name of mango is Mangifera indica.● This nomenclature is in Latin and internationally accepted.● The advantage of this system is that it helps to avoid confusion that occurs due to

presence of various common names as per various regions of world.

Evidence for the new system of classification

Earlier organisms are classified on the basis of phenotypic characters but sometimes scientist don’t find it a suitable way to classify the organism.● New data about the organisms are collected and analysed by the scientist if it is correct

then change in classification system occurs. E.g. Whales and sharks belong to two different classes even they look similar and both live in sea.

● Molecular evidences also shows how similar organisms are e.g. humans and chimpanzees shares about 94 % of DNA sequence.


● The new system of classification includes three domains Bacteria, Eukarya and Archaea on the basis of phylogeny (evolutionary history) and molecular phylogeny (looks at DNA and proteins for similarity).

Relationship between phylogeny and evolution

● The study of evolutionary history of organisms is known as phylogeny.● It tells about which organism is related to which and how closely related they are.● As per studies, each and every organisms have evolved from a common ancestor or

relative. This can be reflected by phylogenetic tree.● Classification of organisms on the basis of phylogeny is known as cladistics.

Structure of phylogenetic tree

Source : cnx.org

● Root of a phylogenetic tree indicates that an ancestral lineage gave rise to all organisms on the tree. A branch point indicates where two lineages diverged. A lineage that evolved early and remains unbranched is a basal taxon. When two lineages stem from the same branch point, they are sister taxa. A branch with more than two lineages is a polytomy.


Theory of evolution by natural selection and evidences

● According to Charles Darwin, the process of mutation leads to emergence of some desirable and some undesirable characteristics.

● Natural selection selects the individual with fittest characteristic and the process continues until the introduction of new better characteristic in all the organisms.

● This way natural selection leads the evolution of a new traits.● Wallace also contributed to the theory of evolution by natural selection by providing

evidences such as some species use warning colours to deter predators from eating them, therefore they survive and evolved by natural selection.

● Observation of fossil record of an organism shows the gradual changes that occurs in it during evolution. (fossil record evidence)

● Observation of gradual changes in the base sequence of DNA in nucleus as well as mitochondria helps to know how recently closely related species diverged to form new species. DNAs would be more similar if they diverged recently. (DNA evidence)

Different types of variations

Variation are the differences shown by the group of individuals.● Intraspecific variation: exist within a species.● Interspecific variation: exist between different species.● Continuous variation: There is a range of variation. E.g. A tree can have any number of

leaves within a range.● Discontinuous variation: there are two or more categories.each individual falls into one

of these. E.g. humans can be blood group A,B,AB,O.● Variation can be caused by genetic factors (difference in genotype).These variations

are inherited. E.g. Blood groups in humans.● Variations can also be caused by environmental factors (like climate, food, lifestyle).

E.g. pierced ears.

Types of Adaptations

● Behavioral adaptation: To sustain and reproduce itself, organisms acts in certain way. Example: Camouflage of insects according to their background.


● Physiological adaptation: To sustain itself, organisms change their rate of metabolism according to change in temperature of the surrounding.

Example: Hibernation in winter and aestivation in summer.

● Anatomical adaptation: To increase the chances of survival in a particular environment, organisms develop certain structural features.

Example: Hollow bones in birds as a mode of flight adaptation.

Mechanism by which natural selection affects the characteristics of a population● Mutation results into formation of new alleles. All these new alleles may not be

advantageous.● Some of them may be harmful or not so beneficial.Some may not be able to adapt to

changing environment. Here comes the role of natural selection.● Nature will select the best allele which is fittest for survival as well as for successful

reproduction.● Therefore, the fittest or most advantageous allele of a gene will be inherited by

members of next generation.● After several generations, this new advantageous allele of a particular gene will be

more in number compared to the disadvantageous allele thus increasing their frequency in the population.

● The disadvantageous allele/alleles will be gradually eliminated from the population by the process of natural selection.

Implications of pesticide resistance in insects and drug resistance in microorganisms for humans● Pesticide resistance means the pest has developed resistance against a particular

pesticide and would not be killed by it. This resistance passed on to generation and lead to evolution of pesticide resistant insects.

● To kill those insects farmers have to use broader pesticides which may kill beneficial insects too.

● It needs a lot of time and money to develop new pesticides which are effective for a particular pest.

● Another case is antibiotic resistance in various infectious bacteria and microorganisms. To treat the disease, it needs a lot of time by doctors to figure out which drug will be effective.

● It also needs a lot of time and money to develop drugs which are effective for a particular infectious microorganism.


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Module 4: Biodiversity, evolution and disease