Plant Structure:

Structure of a typical plant cell:

-Has many futures in common with an animal cell.

-Same basic chemical make-up of cell membranes.

-Similar properties.

-Control movement of substances in a similar way.

1) The Plant Cell Wall:

-It is the tough outer layer around plant cells.

-Causes plant cells to appear more regular and uniform, than animal cells, in their appearance.

-Gives plants strength and support.

-Made up mainly of cellulose (similar to complex carbs such as starch and glycogen), which is composed of long chains of glucose joined by glycosidic bonds.

-Glucose comes in two different forms due to different arrangement of atoms on the side chains of the molecule.

-The different isomers form different bonds between neighbouring glucose molecules which affects the polymers they form.

-In starch, the monomer units are a-glucose.

-In cellulose, the monomer units are b-glucose held together by 1,4 glycosidic bonds where one of the monomer units has to be turned around so that bonding can take place.

-The linking of b-glucose molecules means that the hydroxyl groups stick out on both sides of the molecule.

-This means hydrogen bonds can form between the partially positively charged hydrogen atoms of the hydroxyl groups and the partially negatively charged oxygen atoms elsewhere in the molecule.

-This is known as cross-linking and holds neighbouring chains firmly together.

-Many hydrogen bonds form making cellulose a material with considerable strength.

-Cellulose molecules do not coil or spiral – they remain as very long, straight chains.

-In contrast, starch forms compact globular structures that are useful for storage.

-This difference between starch and cellulose gives them very different properties.

-Starch is an important source of energy in the diet for many animals.

-Most animals do not possess the enzyme needed to break the 1,4 glycosidic bonds between the molecule of b-glucose and can therefore not digest cellulose.

-Cellulose in plant food is what acts as roughage or fibre in the human diet.

-However, some animals may possess the enzymes needed to digest cellulose.

-In the cell wall, groups of 10-100,000 cellulose molecules form microfibrils.

-These can be seen under electron microscopes.

-These cellulose fibrils are laid down in layers held together by a matrix (surrounding substance) of hemicelluloses and other short-chain carbohydrates that act as a kind of glue binding to each other and to the cellulose molecules.

-Affects the strength of the cell wall.

-Sugars involved include mannose, xylose and arabinose.

-The combination of the cellulose microfibrils in the flexible matrix makes a composite material, combining the properties of both the materials into the plant cell wall.

-The cells are firm (turgid) most of the time, giving the strength to support the plant in a vertical position.

-The plant can wilt when in shortage of water becoming flaccid.

-The microfibrils are arranged in spirals around the cell wall (individual cellulose molecules do not spiral).

-The more vertical the spirals, the closer the turns and the stronger the structure of the cell in the vertical direction.

-Strength needed to act against gravity pulling plant down.

-Cell wall is usually permeable to everything dissolved in water.

-The cell wall, however, can become impregnated with suberin (waxy, waterproof compound) or with lignin to produce wood.

-These compounds affect permeability of the wall.

-The plant cell wall consists of several layers.

Middle Lamella:

-First layer of plant cell wall to be formed during cell division.

-Made largely of pectin (polysaccharide which acts like glue and holds the cell walls of neighbouring plant cells together).

-Pectin has lots of negative carboxyl groups and these combine with positive calcium ions to form calcium pectate.

-This binds to the cellulose that forms on either side.

-The cellulose microfibrils and the matrix build up on either side of the middle lamella.

-These walls are very flexible, with the cellulose microfibrils oriented in a similar direction.

-They are known as primary cell walls and as the plant ages secondary thickening may take place giving rise to a secondary cell wall.

-Cellulose microfibrils are laid densely at different angles to each other.

-This makes the composite material much more rigid with hemicelluloses further hardening it.

-In some plant, lignin is added to the cell walls to produce wood which makes the structure even more rigid.

-Within the structure of a plant there are many long cells with cellulose cell walls that have been heavily lignified.

-These are known as plant fibres and are used in many different ways by mankind.

Plasmodesmata:

Sites of intercellular exchange through cytoplasmic bridges between plant cells.

-Involved in close communication with adjacent plant cells.

-These are special cytoplasmic bridges in which intracellular exchange occurs.

-Produced during cellular mitosis.

-Cells do not divide completely with and threads remain between them.

-These threads pass through gaps in the newly formed cell walls and signalling substances can pass through from one cell to another through the cytoplasm.

-The interconnected cytoplasm of the cells is called the symplast.

Plant Cell Organelles:

Vacuole:

-A fluid-filled space inside the cytoplasm surrounded by a membrane called the tonoplast.

-Filled with cell-sap, a solution of various substances in water.

-The vacuole is involved in maintaining the cell shape by osmosis (cell-sap causes water to move in) keeping the cell turgid and the whole plant upright.

-Can also be used to store proteins, pigments, enzymes (in some), waste products and other chemicals.

-If the tissue is heated, substances stored may leak out due to changing of membrane characteristics.

Chloroplasts:

-They are disc-shaped structures appearing green to the presence of the light-harvesting molecule chlorophyll.

-Involved in photosynthesis and the production of carbohydrates.

-Enable plants to make their own food.

-Not all plant cells contain chloroplasts but almost all contain genetic information to make chloroplasts.

-Occur in the palisade and spongy mesophyll layers of a leaf.

-Formed from a type of relatively unspecialised plant ‘stem cell’ known as a leucoplast.

Amyloplasts:

-Specialised plant organelles that develop from plant stem cells known as leucoplasts.

-Used to store amylopectin (a form of starch).

-Colourless.

-This can be hydrolysed to glucose and used to provide energy when the cell needs it.

-Found in large numbers in areas of plants that store starch.

Providing support and transport:

-Primary function of a stem is support, to hold the leaves in the best position to obtain sunlight for photosynthesis.

-Stems also hold flowers in a way that maximises the likelihood of pollination occuring.

-Stem has to provide flexible support in cases of wind and rain.

-They must be able to bend to withstand forces exerted upon them and yet have the strength to stand upright.

-The other major function of stems is the movement of materials about the plant.

-Provide the route along which products of photosynthesis are carried from area of production to parts where they are needed.

-Water moves through the stems from the roots up to the leaves, carrying mineral ions needed for the synthesis of more complex chemicals.

-Most stems contain chlorophyll and carry out a small amount of photosynthesis.

The tissues that make up the stems:

Epidermis:

-The outer layer of the stem.

-Plays no role in support but protects the cells beneath it.

-Secrete cutin, a waxy substance which helps to prevent water loss from the stem surface and protects against entry of pathogens.

-May also form hairs which act as an insulating layer, trapping moist air to reduce water loss.

-Some are hooked helping climbing plants to grip.

-Other hairs are protective and may be stiff and bristly or loaded with irritant chemicals.

Parenchyma and Collenchyma:

-Parenchyma cells are packing tissue which make up most of the plant stem.

-These are unspecialised cells but can be modified in ways to make them suitable for storage and photosynthesis (containing chloroplasts in outer layers of parenchyma cells).

-Some of the parenchyma cells are modified into collenchyma and sclerenchyma.

Collenchyma:

-Supporting tissue in plants.

-Have thick primary walls which give the tissue its strength.

-Found around the outside of the stem (just inside the epidermis) giving it plenty of support (remain living and to stretch as the plant grows).

Sclerenchyma:

-Found around vascular bundles in older stems and in leaves.

-Develops as plant gets bigger to support increasing weight.

-Have strong secondary walls made of cellulose microfibrils laid down at right angles.

-Some schlerenchyma form fibres which are very long cells often found in bundles or cylinders around the outside of a stem or root.

-Lignin is deposited on the cell walls of these fibres in either a spiral or ring pattern making the fibres strong yet flexible.

-Strength of the fibre depends on its length and how lignified it is.

-Once the fibre is lignified, the cell contents die as lignin is impermeable to water leaving the fibres as hollow tubes.

-Schlerenchyma cells can also become completely impregnated with lignin when they form sclereids (plant cells with thick lignified walls) .

-May be found in groups in the cortex or individually in plant tissue.

-Sclereids are joined together by pits.

Vascular Bundles consist of the following tissues:

Xylem:

-The xylem tissue carries water and dissolved minerals from the roots to the photosynthetic parts of the plants.

-The movement in the xylem is always upwards.

-Made of many different cells most of which are dead.

-Long tubular structures called xylem vessels are the main functional units of the xylem.

Phloem:

-The phloem is living tissue made of phloem cells which transport the dissolved product of photosynthesis (sucrose) from the leaves to wher it is needed for growth ot storage (as starch).

-The flow of the phloem can be either up or down.

-Cambium is a layer of unspecialised cells which divide to give rise to more specialised cells which form both the xylem and phloem.

Xylem:

-Starts off as a living tissue.

-The first xylem form is the protoxylem.

-It is capable of stretching and growing as the walls are not fully lignified.

-The cellulose microfibrils in the walls of the xylem vessels are laid vertically which increases the strength of the tube and allows it to withstand compression forces from the weight of the plant pressing down on it.

-As the stem ages and the cell stops growing, increasing amounts of lignin are laid down in the walls.

-As a result, the cell becomes impermeable to water and other substances.

-The tissue becomes stronger and more supportive but the contents of the cells begin to die.

-This lignified tissue is known as the metaxylem.

-The end walls between the cells largely break down so the xylem forms hollow tubes running from the roots to the tip of the steams and leaves.

-Water and minerals are transported from one end to the other in the transpiration stream.

-Water moves out of the xylem into surrounding cells either through unlignified areas or through specialised pits (holes) in the walls of the xylem vessels.

-Lignified xylem vessels are strong and play an important role in plant support.

-In smaller, non-woody plants, parenchyma cell turgidity provides support.

-The movement of substances around plants is usually called translocation.

-Plants use a variety of physical processes to help move materials along the tubes.

-Plants have to move water up from the roots where it is absorbed to the aerial parts.

-The xylem has a very narrow diameter leading to large resistance however it shows water to have great speed while moving through the xylem.

Transpiration:

-The movement of water in the xylem depends on transpiration.

-Transpiration is the loss of water vapour from the surface of a plant, mainly leaves.

-Once in leaves, water moves by osmosis from the xylem into the veins of the leaves into the mesophyll cells.

-Water then evaporates from the cellulose walls of the spongy mesophyll into the air spaces.

-The water vapour moves through open stomata into the external air along a diffusion gradient.

-Each leaf has a layer of still air around it which the water vapour has to diffuse through before it is swept away by moving air.

The Transpiration Stream:

-When water is lost from the leaves, it moves by osmosis across the leaf from cell-to-cell all the way from the xylem.

-When molecules of water leave the xylem to enter a cell by osmosis, this creates tension in the column of water in the xylem.

-This tension is transmitted down in the roots.

-Due to cohesion of water molecules.

-Dipolar nature of water and hydrogen bonds between water molecules gives the column of water high tensile strength so it is less likely to break.

-Molecules adhere strongly to the walls of the narrow xylem.

-The combination of cohesion and adhesion pulls the whole column of water in the xylem upwards.

-Replaces water lossed by transpiration.

Movement of Water:

-Important component of soil is soil water.

-Water is absorbed mainly by younger parts of the roots where the majority of the root hairs are found.

-Microscopic root hairs are extensions of the membranes of the outer cells of the root.

-Greatly increase surface area of absorption.

-Root hairs allow close contact with soil particles.

-The uptake of water by the root hairs depends on the concentration gradient.

-Water moves from the soil into the root hair cell by osmosis.

-This makes the root hair cell more dilute than its neighbour.

-Water moves from cell-to-cell by osmosis across the root to the xylem.

-The detailed mechanism is far more complicated.

-There is a concentration gradient across the root from the root hair cells to the cells closest to the xylem.

This is as a result of two effects:

i) Water is continually moved up the xylem by transpiration.

ii) Solute concentration increases in the cells across the root towards the xylem.

-The water does not simply flow from one cell to another.

-There are three alternative routes into the xylem vessels.

1) Vacoular Pathway:

-Water moves by osmosis across the vacuoles of the cells of the root system.

-Water moves down a concentration gradient from the soil solution to the xylem.

2) Symplast Pathway:

-Water moves down concentration gradient from the root hair cells to the xylem.

-Water moves through interconnected cytoplasm of cell through plasmodesmata which go through pores in the cellulose cell wall.

3) Apoplast Pathway:

-Water is pulled by attraction between water molecules across ajdacent cell walls (apoplasts) from the root hair cell to the xylem.

-Because of the loose open-network of cellulose, up to half of the volume of the cell wall can be filled with water.

-As water is drawn into the xylem, attraction between the molecules ensures that more water is pulled from the adjacent cell wall and so on.

-Mineral ions in soil water is also drawn through the apoplast pathway.

-Water moves across cell walls until it reaches the endodermis, which contains a waterproof layer called the Casparian strip.

-Whichever route the water and minerals have taken, once they reach the Casparian Strip, they enter the cytoplasm of the cell temporarily.

-Mineral ions may have to move into vacuoles by active transport.

Root Pressure:

-Transpiration is a passive process (lacks need of energy).

-However, when metabolism is inhibited, water transport is affected.

-Suggests there is a more active mechanism.

-During the night, when transpiration is really low, droplets of water are forced out of the leaves by a process known as ‘guttation’.

-This is a result of root pressure, root sap will continue to ooze even if cut off.

-Involves active transport.

-Current model suggests active secretion of salts into the xylem which increases concentration gradient across the root.

-This increases the movement of the water into the cells by osmosis.

Why do plants need minerals?

-Certain minerals are needed to synthesise substances essential for healthy growth.

-Plants must extract these minerals from the soil.

1) Nitrogen:

-Used to make amino acids and therefore proteins.

-Proteins needed to make essential enzymes.

-Also, nitrates are needed to make DNA and many hormones.

-When plants lack nitrates, their older leaves turn yellow and die along with stunted growth.

2) Calcium:

-Combine with pectin in the middle lamella to produce calcium pectate which holds plant cells together.

-Play vital role in permeability of cell membranes.

-When plants lack calclium, growing points die back and young leaves are yellow and crinkly.

3) Magnesium:

-Needed to produce green pigment chlorophyll.

-Also needed for activation of some enzymes and synthesis of nucleic acids.

-When plants lack magnesium, yellow areas develop on older leaves and growth slows down.

4) Phosphates:

-Needed for phosphate groups in ATP and ADP.

-These are involved in energy transfers of cells.

-Important to some structural molecules that offer support to plant cells and to the nucleic acids.

-When plants lack phosphates, they have very dark greens with purple veins and stunted growth.

Food for Thought:

-People have always exploited plants to provide material for building, clothing, medicines, food and drinks, dyes and for fuel.

-Plants are central to the human diet.

-Provide macro- and micronutrients.

-Also contain fibres which helps the working of the gut.

-Some plants are grown as food staples – these are basic energy-supplying foods in the diet.

-Contain many amyloplasts (store starch).

-Many seeds contain very rich stores of starch.

-These seeds, therefore, provide plenty of carbohydrates, some proteins and oils as well as small amounts of valuable micronutrients.

-We use other seeds, such as sunflowers, linseed, oil-seed rape and many nuts, for the oils they contain.

-Pulses (beans, peas, lentils) provide much of the protein requirement for people who eat little or no meat.

-Fleshy, succulent fruits are important as sources of sugar and vitamins.

Fibres:

-Plant fibres have been used for years to make rope, paper and cloth.

-Fibres usually have to be extracted from the plant first.

-These fibres are very long sclerenchyma cells and xylem tissue which are very tough.

-Cellulose is not easily broken down by enzymes or chemicals.

-However, the matrix of pectates and other compounds around the fibres (including lignin) can usually be dissolved or removed.

-Plant fibres have great tensile strength - they cannot be easily broken by pulling.

-This, along with their flexibility, makes them very useful.

-Usually occur in bundles of fibres which are much stronger than the individual cells.

How Fibres are processed to make products:

-Paper is usually made from fibres from wood.

-Wood fibres are not easy to extract because the matrix around the cellulose fibres contains a lot of lignin.

-Fibres are soaked in strong alkalis to produce a pulp of cellulose and lignified cellulose fibres.

-This pulp is pressed onto frames where they dry to form paper.

-Traditional methods included retting.

- Material around fibres was broken down by natural actions of decomposers.

-Natural decomposers have been replaced by enzymes and chemicals to speed up process in developed countries.

-The best known and most widely used of natural fibres is cotton.

-One of the great advantages of cotton is that it is produced in the form of almost pure fibres.

-So, no need for retting or other treatment.

-However, long cotton fibres are not useful on their own.

-Spinning pulls out the single fibres, twists them together to form a long thread.

-Resulting threads are woven together to make a fabric.

-Happens on a massive industrial scale.

-Synthetic fibres were made.

-They were cheap, exciting, didn’t crease and relatively hard-wearing.

-However, they were not able to breathe and cannot soak up body fluids, such as sweat.

-They are made from chemicals derived from a non-sustainable resource which gets increasingly expensive and is rapidly being used up.

Sustainabiity:

-Using materials which can be replaced.

-Increasing important idea.

-Plants are vital in developing sustainable resources as they soak up carbon dioxide.

-More comfortable to wear as they are more absorbent.

-The properties of plant products mean they will play an increasingly large role in providing what we need in the future.

Wood:

-Composite material made up of lignfied cellulose fibres embedded in hemicelluloses and lignin.

-The great benefit of a composite material is that it has the properties of both materials.

-The cellulose fibres make the wood very resistant to compression so it is excellent for weight-bearing in buildings.

-Wood also retains some of the flexibility of the matrix and doesn’t tend to crack.

-Can be used to: make baskets, fencing hurdles, boats, cricket bats, furniture, building homes etc.

-Wood is also a good insulator –homes built from wood need less heating in the winter than a brick house.

-Wood also locks up carbon dioxide.

-It is a sustainable resource if managed properly with replanting programmes.

-Carbon neutral – taking in carbon as it grows and releasing it when it is burnt.

Plastics:

-The use of natural materials in the developed world has declined due to development of new synthetic materials produced from oil-based chemicals, particularly plastics.

-Plastics are synthetic polymers – made up of repeating small units called monomers.

-Vary from soft flexible solids with low melting points to hard brittle materials with very high boiling points.

-They are used to make a wide range of products.

-However, now, modern materials are being developed from natural products as the environmental problems caused by plastics are becoming increasingly obvious.

-Most plastics are polymers made from petrochemicals originating from oil which is a non-renewable source.

-These are non-biodegradable which has led to plastic pollution on a grand scale.

-Some plastics may be melted down and recycled, but many cannot.

Biological Polymers:

-Scientists are increasingly looking at the possibilities of bioplastics – plastics based on biological polymers such as starch and cellulose.

-These have two large potential benefits:

i) They are a sustainable resource – can be grown easily to supply the needs of the bioplastics industry.

ii) They are biodegradable as they are based on biological molecules that can be broken down.

-Bioplastics are increasingly being used to replace traditional plastics.

-A car was made out of plastic in 1941; however the Second World War and the growth of the petrochemical industry took the emphasis away from bioplastics.

Different types of Bioplastics:

-Cellulose-based bioplastics are usually made from wood pulp.

-Largely used to make plastic wrapping for food – cellophane has been used.

-Thermoplastic is the best known and most widely used bioplastic.

-Made from starch extracted from potatoes which is mixed with other compounds to change the properties of the starch.

-One of its main uses in the pharmaceutical industry is to make capsules to contain drugs.

-We can burn bioplastics when their useful life is over.

-This is safer because if allowed to break down naturally, they release methane gas which is 25 times more potent than carbon dioxide.

-Energy released by burning can be used to generate electricity and make more bioplastics.

The Facts:

-Science and technology to produce bioplastics is becoming increasingly available.

-However, plastics made from petrochemicals have extremely useful properties that aren’t easy to achieve in bioplastics.

-Bioplastics are much more expensive than oil-based plastics.

-There is also tension for the use of crops for food, biofuels or bioplastics.

Medicine:

-Over centuries of experimentation, people have found that chemicals produced by plants are also of great benefit in helping the human body fight discomfort or disease.

Extracting the Active Ingredient:

-Salicyclic acid – aspirin – is an everyday example of a drug derived from plants (willow).

-People chewed on willow barks for pain relief.

-Some people even chewed on beaver anal glands to get pain relief, as beavers ate willow bark that contained Salicyclic acid that became concentrated in their anal glands.

-Scientists developed a method to extract and purify the acid.

-One of the major advantages of extracting and purifying the beneficial drugs found in plants is that it is possible to give known, repeatable doses of the active ingredient.

-Enormous masses of plants are needed if we depended on extracting and purifying chemicals.

-Scientists work on isolating healing chemicals from plants, analysing their chemical structure and then synthesising the drug on an industrial scale.

-In many cases, the original plant product is modified to make it even more effective.

-Chemicals may also prevent rather than only heal.

-Allows people to work in malaria-infested sites.

The work of William Withering:

-British doctor and botanist.

-In 1775, a patient came to him complaining of a serious heart condition.

-Withering had no effective treatment, so the patient went to see a local ‘wise woman’, who used herbs to cure a number of conditions.

-He bought the recipe, seeing how it helped the patient.

-Discovered that foxgloves were the active ingredient.

-Killed some patients because of digitalin poisoning however he got the dose right in the end.

Testing Promising New Medicines:

-These days, medicines brought onto the market have undergone several years of research and development.

-The new medicine has to be:

i) effective

ii) safe – non-toxic and without any unacceptable side-effects

iii) stable – able to be stored for some time and used under normal conditions

iv) easily taken and removed from your body

v) capable of being made in a large scale

-When scientists think they have a compound that might make a useful medicine, they patent it.

-This patent gives the inventor to be the only one to make and sell their invention for the next 20 years.

-The compound is tested on cell cultures, tissue cultures and whole organ cultures to see if it has the effect it was designed to have.

-Many chemicals fail at this stage because they don’t work in living tissue or have harmful effects.

Drug Development and Animal Testing:

-Before a drug can be tried on people, it needs a way of getting into them.

-Drug has to be stable and not able of breaking down to form something toxic.

-At this stage, the potential drug will be tested on animals to find out how it works in a whole organism.

-This will also show if the drug gets taken into cells, if it is changed chemically in the body and if it is excreted safely.

-Mammals are used for drug testing as they are as similar as possible to humans.

-The most widely used mammals are rats and mice.

-Some tests have to be carried on both rodents and non-rodents.

-These tests are expensive and time consuming and centre of much ethical debate.

-Wherever possible, animals are replaced by tissue cultures and computer models.

-These tests are also refined to cause minimum distress.

-However, at this moment, the information from computer modeling and from tests on cell or tissue cultures is not sufficient enough to test drugs safely on people without animal testing.

-So, the law states that animal testing must be carried out at this stage.

-Many people have ethical objections against this but the use of rodents is perceived as much less emotive.

Clinical Trials:

-If the animal testing is successful, the first human trials follow.

-Before trying the drug on people, you have to apply for a clinical trial authorisation with the “Medicines and Healthcare products Regulatory Agency (MHRA)”.

-They take decisions about the testing and licensing of new medicines.

Phase 1 Trials:

-Trial in which a new drug is given to a small number of healthy volunteers.

-To check that the drug works as expected and doesn’t cause any unexpected side-effects.

-Scientists continue to look for longer-term effects in previous animal testing.

-If the drug is successful, it moves onto phase 2.

Phase 2 Trials:

-Trial in which a new drug is given to a small group of volunteer patients affected by the condition the drug is designed to treat.

-Between 100-500 patient volunteers are given the new drug.

-Doctors see how the new medicine affects the disease in a real patient.

-Volunteers are monitored closely to find out more about the ideal dose, the effectiveness of the drug and any side-effects.

-Success at this stage means the compound has a good chance of becoming a useful medicine.

Phase 3 Trials:

-Trial in which a new drug is used with a large group (5000+) affected by the condition the drug is designed to treat.

-Confirm effectiveness and safety of drug.

-Number of patients involved is large, so there is a better chance of any unexpected adverse side-effects to show up.

-Last phase before the drug is fully approved.

-Marketing authorisation application is sent to the MHRA in UK to seek approval for the medicine to be sold in Europe.

-Phase 2 and 3 trials are normally carried out as double-blind trials (neither patient nor doctor know whether the drug given is the new medicine, a control medicine or a placebo).

-Placebos are used because patients often appear to respond to a treatment they believe will do them good.

-This is known as the placebo effect.

-It is difficult to achieve a complete set of results in clinical trials because many patients stop taking the medicine for various reasons or do not take it regularly.

-The number of patients enrolling in a trial is not necessarily the number of patients who complete it.

-In some trials, the new drug or drug combination is so successful that the trial is halted early.

-The benefits of a medicine must always outweigh the risks.

Biodiversity:-Biodiversity describes the number and variety of different organisms found in an area.

-The earth’s biodiversity is decreasing rapidly.

Naming Organisms:

-Biologists classify organisms to identify them and to show the way in which they are related to each other.

-Every organism is given two Latin names – the genus (a genus is a group of similar species) and the species name.

What is a Species?

-Described as a group of closely related organisms that are all potentially capable of interbreeding to produce fertile offspring.

-Classifying living organisms is central to monitoring changes in species in any given area around the world.

-Scientists make decisions about which organisms belong in the same species and how they are related in a number of ways.

-Originally, scientists look at the organism’s morphology (inner and outer appearance).

-However, today there are more sophisticated ways of comparing organisms.

-Although DNA, RNA and proteins are broadly similar across organisms, they reveal differences when they are broken down to their constituent parts.

-Scientists use these differences to build up a new science of Molecular Phylogeny.

-This is the analysis of different chemicals and genes in different organisms to define interrelationships.

Other definitions of Species include:

-Ecological species: species based on the ecological niche which they occupy.

-Recognition species: based on unique fertilisation systems including behaviour.

-Gene species: based on DNA evidence.

-Each of these definitions has its strength and weaknesses.

-Vast majority of the species today are defined by their morphology.

Ecology and Adaptation:

-Organisms do not exist in a vacuum.

-The various species are all part of a complex system of interactions between the physical world and other living organisms which we call ecology.

-The definition of ecology is described as the study of relationships between living organisms and their environment.

-Each species exists in a particular ecological niche.

-An organism’s ecological niche is the role of the organism within an ecological community.

-It describes the role of an organism in the community – sort of like a job description or a ‘way of life’.

-There are different aspects to a niche such as the food niche or habitat niche.

Ecosystem:

-An ecosystem is an environment that includes all the living organisms interacting together, the nutrients cycling through the system and the physical and chemical environment in which the organisms are living.

-Consists of a network of habitats and the communities of organisms associated with them.

Habitat:

-The place where an organism lives.

-When organisms live in only a small part of a habitat it is called a microhabitat.

Community:

-It is all the populations of living organisms living in a habitat at any one time.

Population:

-It is a group of organisms of the same species, living and breeding together in a particular niche in a habitat.

Adaptation to Niches:

-A successful species is well adapted to its niche.

-This means that individuals in that species have characteristics that increase their chances of survival and reproduction which they pass on to the next generation.

-These adaptations may be of different kinds.

-These include anatomical adaptations (adaptations of the anatomy of an animal or plant to conditions), physiological adaptations (adaptations of the biochemistry or physiology of an organism to the environment in which it lives) and behavioural adaptations (adaptations of the behaviour of an animal which gives it selective advantage).

Examples:

1) Anatomical Adaptations:

-Includes thick layers of blubber in seals and whales.

-Includes sticky hairs on sundew plants that enable it to capture insects ready to digest.

2) Physiological Adaptations:

-Diving animals can stay underwater for far longer than non-diving mammals without drowning.

-Once they are underwater, their heart rate drops dramatically.

-Blood is pumped around the body less often and the oxygen in the blood is not used as rapidly.

-Main body muscles work effectively by anaerobic respiration.

-Oxygen-carrying blood is still carried to the brain where it is needed.

-This is known as the mammalian diving response.

3) Behavioural Adaptations:

-Insects and reptiles orient themselves to get maximum sunlight when the temperature is low to warm them up and allows them to move fast enough to escape predators.

-Social behaviour includes hunting as a team or huddling together for warmth.

-Migrating to avoid harsh conditions, courtship rituals and using tools are also other examples.

-Natural selection leads to adaptations which give individuals an advantage in a particular niche.

-If conditions change, those adaptations might not be as successful, and the selection pressure will change.

-This may lead to change in the species or evolution.

-The niche of an organism has a big effect on the genetic make-up of the population.

-Natural selection results in organisms that are adapted to fit a particular niche.

-It is often acting in the genes.

Mutations and Natural Selection:

-Mutations can cause small changes in genes.

-This is the source of variation on which natural selection acts.

-Mutations can increase the size of the gene pool of a population – this is all the different genes (alleles) found in a population.

-The relative frequency at which a particular allele is found in a population is known as the allele frequency.

-This is one way of measuring biodiversity.

-Alleles in a population are affected by natural selection.

-A mutation in a gene may result in a change in the physical appearance of an organism, in its physiology or even in the pattern of its behaviour.

-If this change is advantageous then the frequency of those advantageous alleles will increase.

-If this change is disadvantageous then natural selection will usually result in its removal from the gene pool.

-Sometimes the mutation is neutral (neither increasing or decreasing the success of the individual), in this case it will remain in the gene pool by chance.

For Example:

-When Warfarin was introduced, some rats by chance carried the harmless mutation that caused them to be resistance to this poison.

-The powerful selection factor of the poison resulted in a rapid increase in the frequency of the resistance allele.

-Soon, the majority of the rats were resistant to the poison and a new, more powerful poison had to be introduced.

The Effect of Small Populations:

-Large populations containing many individuals have large gene pools.

-This is because the chance of losing the allele by bad luck is much less.

-For example, in a population of 10 individuals; 1 individual carries an advantageous allele of allowing the individual to run faster.

-If a predator chases the individual, and the individual breaks its leg then the favourable allele will be lost from the population.

-However in a large population, favourable alleles will be carried by a larger number of individuals and the likelihood of these organisms ‘all’ being destroyed is remote.

-So, there is a bigger chance of a potentially useful alleles being maintained in the larger population.

-This is one reason why large, genetically diverse populations are needed to maintain biodiversity.

-Similarly, when a small number of individuals leave the main population and set up a separate new population, genetic diversity is easily lost.

-The alleles this group carries may be a random selection of the gene pool.

-Any unusual genes in the founders of this new population may be amplified as the population grows.

-This is known as the founder effect – process by which any unusual alleles become relatively common in a small population where the founders started off with the particular unusual allele.

Adapting to Change:

-In 1915 in Malpeque bay, the fishermen began to notice amongst healthy oyster catches there were a few diseased oysters.

-The disease spread throughout the entire oyster population with a few disease-free with an allele resistant to the disease.

-Only individuals with this allele were able to survive and reproduce and so the population of healthy oysters jumped back up.

Selection for Change or Stability:

Directional Selection:

-The oysters in Malpeque bay are a good example of directional selection.

-This is when individuals undergo change from one phenotype to another which is more advantageous under the circumstances.

-Occurs anywhere that environmental pressure is applied to a population.

-Frequently seen in populations of insects and plants that are regarded as pests.

-They are sprayed with chemical insecticides or herbicides.

-These chemicals have a devastating effect initially, but directional selection ensures that there is an increase in resistant individuals in the population within few generations.

Diversifying Selection:

-Another variety of selection.

-It is a form of natural selection which results in increased genetic diversity of a population – rather than a trend in one particular direction.

-Occurs when conditions are very diverse and small subpopulations emerge evolve different phenotypes suited to their very particular surroundings.

Balancing Selection:

-It is a form of natural selection that maintains a disadvantageous allele in a population because of benefit to the heterozygote.

-For example, the thalassemia allele affecting haemoglobin is usually lethal if homozygous.

-However, the heterozygous form gives protection against malaria.

-This is known as heterozygote advantage or hybrid vigour (when the heterozygote state for a particular gene gives advantages to an individual).

-When changes in niches cause great changes within a species, we may consider that a new species has evolved from the old one.

Darwin’s Finches:

-Darwin’s finches is a classic example of how the availability of different niches can provide different selection pressures and result in the evolution of several species.

-These birds were discovered by Charles Darwin.

-On the Galapagos Islands, there are a number of feeding niches near the equator for birds.

-These include: small seeds, large nuts and insects living in rotten bark.

-The original finches that arrived at the island were of a single species.

-The islands are 500 miles from land, people suspect a hurricane or storm carried the birds there.

-Within the birds that have arrived at the island, there would have been variation in alleles and characteristics, and different niches on the island would have favoured individuals with different variations.

-So, a bird with a slightly smaller, stronger beak would get food by eating mainly seeds.

-This would enable it to thrive, reproduce and pass on its beak characteristics to its offspring.

-Over generations, natural selection resulted in individuals with small strong beaks ideally adapted to eating seeds.

-Similarly, a finch with a longer, thinner beak would be more successful probing dead wood for insects.

-By exploiting different niches, the finches avoid competing for the same relatively scarce food sources.

-As a result, 14 different species of finch (remarkably similar DNA) have evolved on the Galapagos Islands over several million years from one common ancestral species.

-Food was such an important selection pressure.

-So, it was important to mate with a finch with a similarly shaped beak to pass on the advantageous characteristic.

-Mating with a finch that had a differently shaped beak would produce a variety of offspring that were less well adapted to feeding, so there would also be a selective pressure on choosing the right kind of mate.

-Any other behavioural or phenotypic changes that made choosing the right mate easier were also selected for.

-Selection for features that give reproductive success is known as sexual selection.

-In many species, there are clear anatomical adaptations to help in attracting a mate and so to pass on his genes.

-These include the mane of a lion, the antlers of a stag and the tail of a peacock.

Isolating Mechanisms:

-For different species to evolve from one original species, different populations of the species have to become isolated from each other so that mating, and therefore gene flow, between them is restricted.

-There are a number of ways this could happen:

1) Geographical Isolation:

-A physical barrier that separates individuals from an original population.

-E.g.: rivers, mountains.

2) Ecological Isolation:

-Two populations inhabit the same region but develop preferences for different parts of the habitat.

3) Seasonal Isolation:

-The timing of flowering or sexual receptiveness in some parts of a population drifts away from the norm of the group.

-This can lead to two groups reproducing several months apart.

4) Behavioural Isolation:

-Changes may occur in courtship rituals, displays or mating patterns so that some animals do not recognize other animals as being potential mates.

-This might be due to mutation that changes the colour or patterns of marking.

5) Mechanical Isolation:

-A mutation may occur that changes the genitalia of animals, making it physically possible for them to mate with only some members of the group.

-A mutation may also occur changing the relationship between stigma and stamens in flowers, making pollination between some individuals unsuccessful.

Allopatric Speciation:

-Speciation that results when populations are physically separated in some way.

Sympatric Speciation:

-Speciation that takes place in spite of the fact that the two populations remain geographically close to each other.

Endemism:

-Describes the situation where a species which only occur in a very specific small area such as an island and they are unique to the area.

-The organism is said to be endemic to the area.

-The availability of niches to species that first colonise on the island, the different selection pressure on those niches compared with the ‘home’ environment and the founder effect of a limited gene pool all combine to result in the evolution of new species that occur only in that small area.

-Species become endemic to a specific area because they evolved within the region and haven’t migrated out to other areas.

-Migration is limited by geographical boundaries.

-So islands are more likely to have endemic species, however that doesn’t mean endemism is confined to islands alone.

Examples of Endemism:

Endemic Species of Madagascar:

-Madagascar is a large island off the coast of East Africa.

-Provides good samples of endemism.

-Almost all the species found are endemic to the island.

-These range from the giant baobab trees to ring-tailed lemurs and from bizarre elephant ’s foot plant to the yellow-streaked tenrec.

-The only species that are not endemic are the ones that have been taking the island by people in relatively recent times.

The Isolated Islands of Hawaii:

-The island populations show clearly how living organisms adapt to a particular niche or role in the community.

-The islands are very isolated.

-They have great biodiversity in terms of species numbers – 1000 species of native flowers, 10,000 species of insects, 1000 species of land snails and 100 species of birds.

-In these isolated circumstances, a small group of founder organisms adapted and evolved to take advantage of the different ecological niches that were available to them.

-Places where endemism is common often have a rich biodiversity in terms of species numbers but relatively low genetic diversity.

-This is one reason why areas with many endemic populations are very vulnerable to the introduction of disease.

-Island ecosystems are small and so they are very vulnerable to interference and damage of human beings.

-Over the last 400 years, 75% of the animals extinct were island species.

Biodiversity:

-Biodiversity comprises every form of life, from the smallest microbe the largest animal, the genes that give them their specific characteristics are the ecosystems of which they are part. This includes diversity within species, between species and of ecosystems.

-Decreasing at an alarming rate.

-The number of different species is a useful measure, but the concept of biodiversity is much more far-reaching than this.

-The differences between individuals in species, between populations of the same type of organism, between communities and between ecosystems are all examples of biodiversity.

Why is Biodiversity Important?

-Organisms in an ecosystem are interdependent.

-These ecosystems are linked on a larger scale across the Earth.

-If biodiversity is reduced in one area, the natural balance may be destroyed elsewhere.

-Healthy biodiversity allows large-scale ecosystems to function and self-regulate.

-The air and water of the planet are purified by the action of a wide range of organisms.

-Waste is decomposed and rendered non-toxic by many organisms, including bacteria and fungi, microorganisms in soil and water convert toxic ammonia into nitrate ions which are then taken up and used by plants.

-Photosynthesis plays an important role in stabilizing the atmosphere and world climate.

-Plants absorb vast amounts of water from the soil which then evaporates into the atmosphere by transpiration.

-Plant roots also hold the soil together, affecting how water runs off the soil surface and reducing the risks of flooding.

-Plant pollination, soil fertility and nutrient recycling in systems such as the nitrogen cycle are vital for natural ecosystems as well as farming, and they depend on thriving biodiversity.

-Biodiversity also provides the genetic diversity that has allowed us to develop the production of crops, livestock, fisheries and forests, and enables further improvements by cross-breeding and genetic engineering.

-This helps us to cope with problems arising from climate change and disease.

-Biodiversity also provides the potential of plants to produce chemicals that are important in many areas of human life.

Are some species more important than others?

-The media usually express important of extinction and loss of biodiversity when it comes to large, charismatic animals such as pandas, elephants, whales and tigers.

-However, plants lower down the food chain have an important role in preserving biodiversity.

-Understanding the complex feeding relationships can help us protect whole ecosystems.

Example:

-Figs are staple food for hundreds of different species in many different countries.

-Animals from tiny insects to birds and large mammals feed on everything from the bark and leaves to the flowers and fruits.

-Each species of figs have a specific fig wasp that has evolved to pollinate only that type of fig.

-So, without the fig wasps, the fig trees would die out and many other species would be affected.

-The figs and pollinators are closely linked, and problems for each of them would result in a huge effect with a great loss of biodiversity.

-The fig wasps have a vital role.

Keystone Species:

-A species that has a major effect on its environment even if they are not the most obvious species in the area.

-A large number of other species depend on a keystone species for their survival.

-The fig wasps would be an example of a keystone species.

Another Example:

-Sea otters play an important role in preserving giant kelp forests in the ocean.

-Kelp forests provide a home for a wide range of other species .

-Kelp, itself, is also the main food of purple and red sea urchins.

-When there are a lot of sea urchins free from predators, they roam the ocean floor and eat kelp as it starts to grow.

-This keeps the kelp short and stops forests developing which in turn reduces biodiversity.

-However, sea otters are major predators of sea urchins, so sea urchins tend to hide to avoid predators.

-This allows kelp to grow and as it forms, bits break off and fall to the bottom and provide food for sea urchins hiding in crevices.

-Sea otters are a keystone species here however they are vulnerable to human hunters.

-Scots pine is the keystone species in the Caledonian forest.

-A huge number of species depend on these trees.

Are some places more important than others?

-In terms of number of species, around the world biodiversity varies enormously.

-Wet tropics are generally areas of highest biodiversity.

-As you move away from wet tropics, the species diversity tends to fall.

-Some areas were identified as biodiversity hotspots – an area which is particularly rich in different species.

-Species richness is not the only important factor.

-Another important criterion is endemic species in an area.

-Areas of biodiversity are not always the same as areas with endemic species.

-This makes it difficult to prioritise areas for conservation.

-Many ideas

have been published as theories about why particular areas have particularly rich biodiversity.

-Many of these theories have been eliminated as they apply to organism or are not support by evidence.

-A very stable ecosystem allows many complex relationships to develop between species.

-High levels of productivity (when photosynthesis rates are high) can support more niches.

-A paper published suggested that species diversity is linked to productivity through a speeding up of the evolutionary process.

-In other words, in areas where organisms grow and produce more rapidly, more mutations can occur which introduce more variety, enabling organisms to adapt to particular niches and evolve to form new species.

-The risks to biodiversity are not evenly spread around the world.

-Some areas are more vulnerable to damage and loss, especially small areas such as islands, rainforests, coral reefs, bogs and wetlands.

-Many of these areas are biodiversity hotspots, so if they are damaged many species will be lost.

-Every time a species is lost, the world’s biodiversity decreases.

-Biodiversity is often measured by species richness – the number of species in the area.

What do we measure?

-It isn’t necessary to observe every different type of organism in an area to build up a picture of the health of the ecosystem.

-Certain species are susceptible to change in biodiversity.

-These species are referred to as indicator species or bioindicators.

-These species are particularly sensitive to change and so can be used to indicate problems in an area which might lead to loss of biodiversity.

-Changes in these species reveal changes in the overall balance of the ecosystem.

-The size of populations of different species can also give us an idea on the biodiversity.

-If there aren’t enough organisms in a population, it may be difficult to find a mate.

-There won’t be a sustainable breeding population.

-Also, if gene pool is reduced in a way that many individuals share the same alleles, faulty traits show up more and there is less variety.

-So, introduction of disease is able to wipe out a small population.

-The population size of keystone species is also important to monitor.

-Any significant increase or decrease can have major effects on the whole food web.

When to measure biodiversity?

-Biodiversity is not constant.

-Animal species in an area can vary with the time of day, as well as seasons.

-Due to migrating of birds, different plant species fertilizing at different times etc.

-When measuring, you need to assess the number of species in the area and the size of their populations.

-You also need to identify them correctly.

Measuring Genetic Biodiversity:

-The genetic variety within a population is also an important measure of biological health and wellbeing.

-Without variety, a population is vulnerable (disease, human interference etc.).

-With modern technology, it is possible to build a clear model of genetic diversity (variety of genes and alleles) within a population.

-This includes analysing the DNA and comparing particular regions for similarities and differences.

-Cheetahs have low genetic diversity.

-Vulnerable to being wiped out by a disease or change in their environment.

-As habitats disappear, there are serious worries about the survival of species.

-Models of molecular phylogenetic relationships between related organisms based on DNA and other evidence has proved to be a very useful tool for genetic biodiversity.

-Maps showing species richness and genetic variety are important.

-Comparison allows confidence in choosing best area to preserve biodiversity.

-Can be generated for overall biodiversity or for the diversity of particular groups of animals and plants.

-Can be produced for the whole worlds, individual countries or for smaller local areas.

-This data is valuable as it can be used to highlight areas that need protection.

-Provides a way of monitoring changes in biodiversity, with regular updating, in any particular area or worldwide.