UNIT FOUR

PHOTOSYNTHESIS This is the process by which green plants make their own food. The main organ involved is the leaf, although green herbaceous stems may contain cells with large number of chloroplast. The external features of a leaf would be as follows:Pg3 GEB The internal structure of a leaf would be as follows:-

The functions of the different structures of a leaf are:(1) Epidermis: - It gives rise to the waxy cuticle which prevents excessive transpiration. - It prevents the plant from mechanical injury. - It prevents invasion by micro-organisms. (2) Palisade mesophyll layer: - It is the site for photosynthesis. (3) Spongy mesophyll layer - Gaseous exchange - Photosynthesis - Storage of oxygen (4) Xylem: - Provides the leaf with mineral salts and water. (5) Phloem: - Translocation of manufactured food e.g sucrose, amino acids etc (6) Guard cells: - Control of opening and closing of stomata. The leaf is adapted to photosynthesis as follows: They are broad, thus provides a large surface area for absorption of light. The palisade is located near the upper surface of the leaf where they obtain maximum light for photosynthesis.

They have a network of veins: xylem which supplies water for photosynthesis, they also provide support to the leaf lamina where they can obtain maximum light. A large number of stomata present on the lower epidermis for maximum exchange of gases. They are thin thus reducing the diffusion distance for gases. The upper waxy cuticle is transparent therefore allowing light to pass through.

Palisade cells: This is where photosynthesis takes place and has the following structure:Pg 5 GEB

Within the palisade cells photosynthesis is centered within the chloroplast organelles which have the following structure:-

NB: It has the following structures in relation to photosynthesis: Have a variety of pigments which trap a variety of wavelengths. Have many thylakoids / membranes which provide a large surface area for the attachment of pigments. Thin membranes which allow passage of light. Has stroma where there are enzymes required for process of photosynthesis.

Pigments: The different types of pigments that can be found in a chloroplast by chromatography include:(a) Chlorophyll a (b) Chlorophyll b (c) Carotene (d) Fucoxanthin (e) Phycobilins etc NB: Each pigment has a particular wavelength of light it absorbs. The photosynthetic pigments can be divided into two main groups:(1) Primary pigments: They are of two types both of which are specialized forms of chlorophyll a, one is designated as P680 and the other as P700. (2) Accessory pigments: They include all the other forms of chlorophyll and carotenoids. They pass on their energy to the primary pigments which emit electrons which cause the light dependant reaction to take place. PHOTOSYSTEMS: This refers to how photosynthetic pigments are organized and there are two main groups:PSI (photosystem I) which contains the primary pigment P700 + accessory pigments. PSII (photosystem II) which contains P680 + accessory pigments. THE PROCESS OF PHOTOSYNTHESIS It occurs in two stages:(i) (ii) The light dependant stage which requires light energy and results in the production of ATP and NADPH (reduced nicotinamide adenine dinucleolide phosphate). The light independent stage in which the NADPH is used to reduce carbon dioxide to carbohydrate and ATP is used.

Light dependant stage: 2eElectron acceptor 2 2e Electron carrier System 2ADP Electrons 2ePSII 1 P680 light light P700 6 2eH2O O2 7 2ATP 5 8 2H

NADP

NADPH +H+

3 PSI 4

2H+ protons

1. Light energy is trapped in photosystem II and boosts electrons to a higher energy level. 2. The electrons are received by an electron acceptor. 3. The electrons are passed from the electron acceptor along a series of electron carriers to PSI. The energy lost by electrons is captured by converting ADP to ATP. Light energy has thereby been converted to chemical energy. 4. Light energy absorbed by PSI boosts the electrons to an even higher energy level. 5. The electrons are received by another electron acceptor. 6. The electrons which have been removed from the chlorophyll are replaced by pulling in other electrons from a water molecule. 7. The loss of electrons from the water molecule causes it to dissociate into protons and oxygen gas (photolysis). 8. The protons from the water molecule combine with the electrons from the second electron acceptor and these reduce NADP.

9. Some electrons from the second acceptor may pass back to the chlorophyll molecules by the electron carrier system yielding ATP as they do so. This process is called cyclic photo-phosphorylation. Light independent stage: ATP From the light Dependant stage ADP 4 Calvin cycle ATP

NADPH +H+ 5 Triose phosphate 3c

Glycerate-3-phosphate 3

3c

NADP+ Oxidized returns To light dependant

Glyceraldehyde-3Phosphate (GALP) ATP ADP 6 Hexose sugar Ribulose-biphosphate 2 5c

7 Starch

1 Carbon dioxide 1c

1. Carbon dioxide diffuses into the leaf through the stomata and dissolves in the moisture on the walls of palisade cells. It diffuses through the cell wall, membrane, cytoplasm and chloroplast membrane into the stroma of the chloroplast.

2. The carbon dioxide combines with a 5-carbon compound called ribulose biphosphate with the help of an enzyme called RUBISCO (ribulose biphosphate carboxylase) to form an unstable 6- carbon intermediate. 3. The 6 carbon intermediate breaks down into 2 molecules of 3-carbon glycerate 3- phosphate (GP). 4. Some of the ATP produced during the light dependant stage is used to help convert glycerate 3- phosphate into triose phosphate (glyceraldehydes 3 phosphate) GALP 5. The reduced NADPH +H+ from the light dependant stage is necessary for the reduction of the GP to triose phosphate. NAPH+ is regenerated and this returns to the light dependant stage to accept more hydrogen. 6. Pairs of triose phosphate molecules are combined to produce an intermediate hexose sugar. 7. The hexose sugar is polymerized to form starch which is stored by the plant. 8. Not all triose phosphate is combined to form starch. A portion of it is used to regenerate the original carbon dioxide acceptor ribulose biphosphate. Five molecules of the 3-carbon triose phosphate can regenerate 3 molecules of the 5carbon ribulose-biphosphate. More of the ATP from the light dependant reaction is needed to provide energy for this conversion. AN EXPERIMENT TO SHOW THE DIFFERENT PHOTOSYNTHETIC PIGMENTS - Grind up leaves with acetone and filter. - Cut a strip of filter paper, such that it does not touch the sides of a boiling tube. - Draw a line with a pencil across the strip of the filter paper at a distance of 1.5cm from one end. - Repeatedly add the filtrate drop-wise until a concentrated spot is formed. - Dip the filter paper strip into a boiling tube containing a solvent, until it just touches the surface of the solvent. - Pigments of different colours travel up the filter paper at different speeds. Draw pg 13 Fig. 5.1.6 STRUCTURE OF ATP It refers to adenosine tri-phosphate. It is the form in which energy is readily available in the body of living things. It consists of:(i) (ii) (iii) Adenine which is an organic base Ribose sugar (pentose) 3-phosphate groups.

The following symbols can be used to show the structure:Adenine ribose phosphate

Energy is obtained from ATP when the 3rd phosphate bond is broken down by hydrolysis with the help of the enzyme ATPase and about 34 KJ of energy are released. Meanwhile adenosine diphosphate and a phosphate group are formed i.e ATP ADP + P + Energy 34 KJ

There are two main types by which ATP is formed:-

(i) Energy formed during respiration is used to combine adenosine diphosphate with phosphate i.e C6H12O6 6CO2 + 6H2O + E ADP + P + E ATP

(ii)When electrons are taken by carriers at successfully lower energy levels energy is given out which combines ADP and P to form ATP. NB: The G.P can be converted to pyruvate from where; (i) (ii) (iii) It can be converted to ocetyl co-enzyme A which combines with Oxaloacetate which later gives rise to x-ketogluterate which is an amino-acid. These aminoacids now combine to form proteins. Fatty acids are formed which combine with glycerols from the 6c phosphorylated sugar to form lipids. Pentose sugar like ribose and deoxyribose are formed which help in the formation of nucleic acids.

FACTORS THAT AFFECT THE RATE OF PHOTOSYNTHESIS They are:(i) Light intensity (ii) Carbon dioxide concentration (iii) Temperature

A limiting factor is that which when increased increases the rate of reaction e.g from the graph given next page light intensity is the limiting factor between points A and B, while between B and C light is not a limiting factor, but other factors e.g Co2 concentration, temperature etc.

Rate of Photosynthesis B C

A Light intensity Use the following graph to give the limiting factors in each of the graphs drawn.

0.13% co2 300c Rate of PhotosynThesis D C B A Light intensity 0.13% co2 200c 0.03% co2 300c 0.03% co2 200c

Graph A Graph B Graph C Graph D

ECOLOGY Terms used:Habitat is a place where an organism normally lives e.g streams, tropical rainforest, grassland etc. NB: Many organisms live only in a small part of the habitat known as microhabitat. Population a group of organisms of the same species living and breeding together in a habitat. Community a group of organisms of different species living together in a habitat at any one time e.g a rock pool may consist of sea weeds, sea anemones, shrimps, crabs etc. ECOLOGICAL NICHE: It is described as the role of the organism in the community i.e its way of life (if the habitat is the address of the organism, the niche describes its profession). Organisms can share the same habitat but occupy different niches e.g fox in a woodland is the top predator, squirrels occupy the large tree-dwelling herbivores, while rabbits occupy the ground and burrowing. ABIOTIC FACTORS: These are the non-living elements of the habitat of an organism e.g (1) Climate This includes sunlight, temperature, rainfall etc. (2) Edaphic (soil) factors like mineral salts, drainage, PH etc (3) Oxygen availability in aquatic environment. BIOTIC FACTORS: These are the living elements of a habitat that affect survival of organisms e.g predators, preys etc.

Biosphere: It refers to that part of the earth that is habitable by living things i.e whole earth and is divided into smaller portions called ecosystems or biomes. Ecosystem: It refers to the interaction between the organism (plant & animals)and the environment (nutrients / physical/chemical/surrounding) to form a self-sufficient system e.g grassland (savannah), tropical rainforest, desert etc. Producers: These are organisms which make their own food but depend on others for food e.g:- Primary consumers (herbivores) they feed directly on plants. - Secondary consumers they depend on primary consumers for their food e.g dog fox etc. - Tertiary consumers these are organisms which depend on secondary consumers as well as primary consumers for their food e.g lion, cheetah etc - Decomposers these are organisms which feed on dead decaying organic matter e.g bacteria, fungi etc - Trophic level refers to a group of organisms which obtain their food in a similar way e.g all producers make their own food thus they belong to the same trophic level in this case it is the 1st trophic level. FATES OF SOLAR ENERGY FALLING ON A LEAF

Some energy is lost by evaporating water on the surfaces of the leaves. Some light energy is reflected by the leaf surface. Some wavelengths of light may penetrate the leaf surface, but they are of no use i.e they are not used at all for photosynthesis. The chemical energy formed is called GPP i.e gross primary production and part of it is used for respiration and the remainder is known as net primary production (NPP). Therefore GPP is total amount of chemical energy captured by green plants in the process of photosynthesis or rate at which energy is incorporated into the plants. While NPP refers to the amount of energy that is available for consumption after respiration has taken place / or energy stored in the body tissue. i.e NPP = GPP R R is the rate at which some of the GPP is used by plant for respiration.

NB: Biomass is the mass of organisms (plants and animals) per unit area of ground or water in a given period of time. Units for biomass thus is Kgm-2yr-1 Since the organisms e.g plants can be dried and burned, then units can be KJm-2yr-1. Since GPP, NPP and Respiration are part of the biomass, then they have same units. Green Bk Pg 25

Energy loss at trophic level: About 10% of energy is transferred from one trophic level to the next. About 90% is lost in various ways as shown below:-

EC = EP+ ER + EU+ EF

EC = Energy consumed EF = Energy lost in feaces EA = Energy assimilated EU = Energy lost in urine ER = Energy lost as heat in respiration EP = Energy of production (for increasing biomass) Some of the energy formed by plants is used for respiration. Not all the parts are eaten by the consumers e.g roots, stems may be too big or plants may be too tall. Not all that is eaten is digested and a lot of energy is lost through undigested food. Some amount of energy is lost through excretion e.g urea which contains energy locked up in it.

Loss of energy along the food chain would be as follows:-

R = Energy loss through respiration C = Consumption by organisms at higher trophic levels. E = Energy lost to detritivores and decomposers through excretion of urine and egestion of feaces. (a) What is the gross primary production of grasses and herbs? Show your working.

(b) What is the photosynthetic efficiency (i.e the efficiency of conversion of incident solar energy to gross primary production)? Show your working.

(c) What is the net primary production of the :(i) (ii) (iii) Seed eating birds Spiders Common green grasshoppers

(d) How much energy is lost via respiration feaces by field mice.

(e) Which of the organisms are heterotrophic?

EFFICIENCY OF ENERGY TANSFER This refers to the proportion of energy used to make biomass (EP) compared with the energy available to an organism in the trophic level. Below is a measure of the efficiency of energy transfer. NB: The efficiency of energy transfer varies e.g it is as low as 0.1% for small herbivorous mammals and about 80% for some MOs. This variation is caused by:(i) (ii) (iii) Effort required to find food. Digestability of the food. Metabolic rate of the organism.

What is the efficiency of energy transfer at:-

(i)

1st trophic level?

(ii)

Organisms in the 2nd trophic level?

(iii)

3rd trophic level?

EFFECTS OF THE ABIOTIC FACTORS OF DISTRIBUTION & ABUNDANCE OF ORGANISMS 1. Light: It influences primary productivity hence consumers directly or indirectly depends on producers thus influencing their distribution. If light levels are low plants may cope by:(a) Reproducing early to avoid shade caused by large plants. (b) Having extra-chlorophyll or pigments sensitive to lower light levels. (c) By increasing the surface area of leaves e.g nettle trees. The photoperiod affects germination, flowering and reproductive behaviour in animals. In aquatic environment, plants are confined to the surface or shallow water at the margins.

2. Temperature: Organisms have optimum temperature where they grow and reproduce at their best. Above or below the range of temperature, reproduction does not occur even if organism survives. Extreme temperatures affect activity of enzymes e.g in plants and ectotherms. Most animals have evolved behaviours and physiological features which ensures their survival. 3. Wind and water currents: Wind increases water and heat loss from the body of organisms, hence for them to survive, they have developed features to be able to cope. Wind can destroy woodlands together with communities within them as in UK in 1987 where recovery took about 20 years. Water currents can be damaging when the strength increases suddenly e.g during flooding. Thus organisms have to be strong swimmers or be able to attach tightly in order to resist the force of the water.

4. Water availability: It depends on:(i) Precipitation (ii) Rate of evaporation and edaphic factors e.g drainage. Where water is scarce, only those organisms with special adaptations will survive e.g camels, catus. Too much water causes massive increase in population size of some organisms. NB: Hydrophytes slow in water Mesophytes survives where water is adequate Zerophytes survives where water is scarce e.g deserts

Oxygen availability: Cold or fast flowing water contains sufficient oxygen to support life. If temperature increases or water becomes still / stagnant oxygen drops affecting survival of populations. Soil air spaces contain oxygen required by the roots for respiration. In waterlogged conditions, air spaces are filled with water and roots are deprived off oxygen and plants may die. However, plants like mangroves have aerial root which is an adaptation for waterlogged conditions.

Edhaphic factors: The structure of soil affects the organisms e.g sandy soil which is loose and have shifting structure allows very little growth unless the plants have massive roots and rhizome network e.g mairam grass. This grass survives physiological drought conditions on sea-shore, the leaves are able to curl with stomata inside thus reducing S/A and hence water loss. Sandy soil is easily warmed, allows fast drainage causing leaching of minerals which in turn reduces population density of plants. In clay it is difficult for water to be drained easily, hence it is easily waterlogged and leaching is not a problem thus supports a wide population. Loam soil which is a mixture of sand & clay is less prone to leaching. Easier to work with and warming it.

EFFECTS OF BIOTIC FACTORS ON DISTRIBUTION & ABUNDANCE OF ORGANISMS Biotic factors are all of the living elements in a habitat e.g

(1) PREDATION: Predators these are organisms which feed on or part of another organism, at times referred to as the prey. As the prey population increases, there is more food for the predators, hence after an interval, the predator population increases. As they increase, then they will be eating more prey that they are replaced by reproduction, thus the number of prey will begin to fall allowing the abundance of prey to increase again. This then reduces the food supply of predators and thus will not produce many offsprings and at the same time will die and the number fall, allowing the abundance of prey to increase again etc. e.g Lynx (predator) and snowshoe hares in Canada.

Population of Predators & preys

Time NB: The oscillations 2. FINDING A MATE: Most animals cannot reproduce by themselves, they require mates (males and females) which in turn have an effect on the abundance of the animals present. In plants, if a seed is dispersed to a new area, it germinates, grows and survives but it is unlikely to be permanent unless other plants of the same species grow or the plant reproduces asexually. 3. TERRITORY: A territory is an area held and defended by an animal or group of animals against other organisms which may be of the same or different species. This ensures that a breeding pair has sufficient resources to raise the young ones.

PARASITISM AND DISEASES: Parasites are organisms which depend on others referred to as hosts for food and shelter. This therefore weakens the host and may cause diseases e.g Dutch elm disease is caused by parasitic fungi spread by elm bark beetles that have destroyed most of the mature elm trees in UK. Diseased animals will be weakened and do not reproduce successfully, while the sick predators cannot hunt well, and the diseased prey animals are more likely to be caught. Some diseases are highly infectious and can be spread without direct contact e.g avian flue. Communities with greater biodiversity normally have less effect of the disease.

NB: Some diseases e.g devil facial tumour disease arose through a mutation in a single Tasmanian devil which reduced the number of chromosomes from 14 to 13. They bite and savage each other when they feed or mate and bits of the deadly tumours are passed on through bites on the face.

COMPETITION: This refers to when two organisms or more are competing for the same resources which is in limited supply e.g abiotic resources like sunlight, mineral salts etc. Biotic resources like territories, nest sites, mates etc. There are two forms of competition:(a) Intra-specific competition: This is competition for limited resources between members of the same species e.g stags compete for females. Meerkats are small mammals that live in family groups where the males and females defend their territory against other meerkats wanting to feed. This may slow growth as well as population distribution. (b) Inter-specific competition: It takes place when different species within a community compete for the same resource. If there is a greater density of one species or faster reproduction rate, the competing species may become extinct e.g goats released on Abingdon Island whose population is high and breed fast compares to tortoise which became extinct in 1960s.

NB: it should be noted that several factors both abiotic and biotic determines distribution and abundance of organisms. DENSITY DEPENDENT AND INDEPENDENT FACTORS Density dependent: These are biotic factors such as competition, predation, diseases etc which increases as the population increases e.g parasitism and diseases are density dependent i.e the more individuals there are in a given area, the more likely that the diseases or parasites can be transmitted between individuals. Breeding success in territorial animals and birds is density dependent as individuals without territories are unlikely to breed. Thus, density dependant factors limit the abundance of species. Density independent: These are abiotic factors such as temperature, light intensity, humidity etc which have an effect on population but which are unrelated to population size SUCCESSION It is a process by which communities of organisms colonizing an area change over time and are replaced by more varied communities. There are two types of succession i.e:(a) Primary succession: This occurs when the starting point is bare rock (or sand dune) normally seen after a volcano eruption. The first plants which grow are called opportunists or pioneer species e.g lichens, algae, moss etc. This help to break the rock into grains and trap organic matter that breaks down to humus. NB: the grains + organic humus forms soil. Soil layer develops, more water and nutrients are retained and become available for plant roots and hence shrubs can grow. The plant biodiversity increases hence the diversity of animals. Finally, climax community is formed e.g woodland where the biodiversity and range of species are generally constant. NB: 1) When a climax community is in equilibrium with the prevailing climatic conditions, then the terms climatic climax community are used. It is a community that remains generally over a long period of time. 2) Plagio climax / biotic / or deflected climax is when humans and other organisms interfere with the climatic climax community and a different equilibrium may be

reached known as biotic climax. This may be brought by constant burning, mowing, grazing and use of weed killers. (b) Secondary succession: This is the evolution of a ecosystem from existing soil that is clear of vegetation e.g after a fire, floods, a river shifting its course or disturbance caused by humans. The several stages would be bare earth. Grass Weeds Grass stage Grass & shrubs Young forests pines, some Young hard wood Mature forests mainly oak

The number of organisms from the beginning is much higher than in primary succession. The climax community depends not only on climatic factors but also on plants and animals that colonize an area i.e 20. Climatic community differs from original 10 climax community.

ZONATION This is when the different several stages of a primary succession can be observed. (i) Down the mountains (ii) Sand dunes At the top of the mountains, soil is very little hence few plants e.g mosses, ferns etc grow. Lower down there is grassland, scrubs and eventually woodland at the bottom. In sand dunes e.g Gibraltar point in UK those communities furthest from the sea in late stages of the succession, while nearest to the sea are the youngest. i.e pg21. Gorse heather Marram Sea holly Pine birch heather & oak Gorse willow

Sand sedge Marram grass CARBON CYCLE

The inefficient transfer of energy between organisms has no problem as there is a constant supply of energy from the sun. For other ingredients of life e.g water, minerals such as carbon, nitrogen etc complex cycles have evolved which ensure that these substances are continuously cycled through ecosystems. It involves biotic phase where

these minerals are incorporated in the tissues of living things and abiotic phase where the minerals are returned to the non-living part of the ecosystem. Diagram of the cycle pg 38 fig. 5.3.1 There is a massive pool of carbon in the carbon dioxide present in atmosphere and dissolved in the water (lakes, rivers, oceans). This carbon is absorbed by plant during the process of photosynthesis and through food chains it is passed on to animals. The carbon dioxide is continually returned to the atmosphere or water during respiration. Some of the dead organic matter is converted to fossil fuels through fossilization while another portion is converted into carbonate rocks through sedimentation.

CARBON SINKS These are reservoirs where carbon removed from the atmosphere is locked up in organic or inorganic compounds. In biotic system, carbon is removed from the atmosphere by photosynthesis and stored in the bodies of living things. In abiotic system, rocks such as limestone, fossil fuels e.g coal, oil, natural gas, humus hold vast stores of carbon. Oceans also act as carbon sink where dissolved Co2 is used for photosynthesis by phytoplanktons. The shells found in most marine organisms require a lot of carbon in their formation as they have a lot of calcium carbonate. Different oceans consume different amounts of carbon e.g Atlantic absorbs about 23% of human-produced carbon, while the southern ocean with a much bigger area absorbs only 9%. The difference could be due to:- (i) water temperature (ii) ocean currents which mixes water with Co2 as they move. NB: the quantity of carbon stored in carbon sinks is measured in petagrams where 1 petagram is 1 x 1015g or 1 billion tones. Pg 39 table 5.3.1 Carbon cycle is a self-regulating i.e the amount of carbon released in respiration and other natural processes and that which is absorbed in photosynthesis remain in balance. However, human activities are offsetting the balance e.g (i) Since industrial revolution coupled with the development of the internal engines used in vehicles, the amount of carbon in the atmosphere is now increasing.

NB: petagrams are units that measure quantity of carbon in carbon sinks. 1 petagram = 1 x 1015g or 1 billion tones GREEN HOUSE GASES

These are the gases responsible for the global warming i.e increase in temperatures on the surface of the earth. They are:(a) Carbon dioxide: It constitutes 9 26% of the green house gases. It is obtained from combustion of fossil fuels by industries as well as motor vehicles. Other human activities e.g deforestation. (b) Methane: It constitutes 4 9% of the green house gases. It has 72 times greater effect than Co2. It is formed:(i) action of certain bacteria on wet decaying organic matter e.g rice paddy fields which are normally waterlogged, have bacteria which release methane as they grow (ii) Bacteria from the digestion of ruminant herbivores e.g cows, deers etc. Cows belch a lot and every time they burp they release methane gas 100 700dm3 per cow per day. However, this depends on:- the breed of the cow e. g freshian, jersey etc - Type of food eaten e.g adding of concentrates to the diet reduces methane emissions per cow as concentrates are easier to digest. - whether the cow is giving milk the higher the number of lactations per cow, the less emissions of CH4. NB: (1) Due to high population, the demand for rice has increased and therefore more methane is produced. Demand for milk has also increased leading to increase in production of methane. (2) A combination of good husbandry, careful breeding and genetic engineering of food plants may result to high production of milk, beef etc and a reduction of methane. (3) Water-vapour contributes 36-70%of green house gases. It is obtained from:Plants during transpiration Evaporation from water bodies e.g oceans, rivers etc Respiration from organisms

(i) (ii) (iii) (4)

Ozone O3 constitutes 3 7% of ghg. It is formed when O2 molecules combine with oxygen atoms in the presence of U.V light. U.V O2 + O O3

Thus preventing the U.V light from reaching the earths surface where they may cause damage e.g skin cancer. (5) CFCs from refrigerators etc. It reacts with ozone layer and therefore making holes.

HOW DOES GREEN HOUSE / GLOBAL WARMING TAKE PLACE? The radiation from the sun reaches the earths surface. However, some radiation is reflected back into the space by atmosphere and by the surface of the earth while some is absorbed by the atmosphere. The infra-red radiation that reaches the earths surface is of fairly shortwavelength that is radiated back at a longer-wavelength. Some of this radiation is absorbed and re-radiated back to the earths surface by green house gas molecules in the atmosphere. This maintains the temperature at the surface of the earth at a higher level which is important for survival of many organisms. Diagram pg 40 fig. 5.3.3 EVIDENCE FOR GLOBAL WARMING 1. Meteorological departments: The UK meteorological office has daily weather records since 1869, although there are written records from diaries and ships which goes back over 100 yrs more. Since mid 1800s, the temperature seems to increase sharply in the northern hemisphere. NB: The other sources of data are called temperature proxies and include:2. Frozen isotopes: This is done in Antarctic and Greenland ice cores. They drill deep down into the ice and analyze the air trapped in the different layers. Records of the oxygen isotopes in melted ice i.e proportion of O16 and O18 reflects the air temperature at the time ice layer was laid down. The ice cores were laid down over 300,000 years ago and from the analysis it appears that at about 140,000 years ago, the surface of the earth was about 60c cooler compared to today and the earth was said to be in ice-age. At around 120,000 years ago temperatures were 1 20c warmer than today. The warmer periods are referred to as interglacials which alternate with ice. 3. Dendrochronology: This is the dating of past events using tree ring growth.

The rings are formed annually by cell division within the ring of cambium tissue. When conditions become difficult, the new cells produced are smaller and the ring formed will be narrower. Thus by counting the rings it is possible to find an approximate age for a tree. Dendroclimatology is the study of what dendrochronology can tell us about the climate in the past e.g wider rings could reflect that temperatures were high although other factors e.g sunshine, carbon dioxide levels, rainfall could have contributed as well. NB: However, by comparing results / data from different places of the same species, then reliable data can be obtained.

4. Peat bogs: They are made of partly decomposed plant materials mainly sphagnum mosses. Peat is acidic, cool and anaerobic and this prevents bacteria from decomposing the organic material. Thus pollen grains, moss spores and plant tissues are preserved. By sampling cores of peat (1 metre of peat is a record of Atleast a thousand years of life in and around the peat bog) Plants and moss growing in an area are affected by climate hence pollen and moss record can give a clear reflection of how climate was e.g (a) Cotton grass and some species of sphagnum mass indicate cool wet conditions. (b) Sphagnum and polytrichum reflect drier conditions. (c) Pollens from horse chestnut trees indicate warmer conditions, while from birch trees shows that it was cooler. 5. Coral reefs: Data from coral reefs can be used to confirm the evidence from trees since the proportion of different isotopes taken up by the coral vary as the sea temperatures change and this gives another valuable proxy record of climate change. 6. Increasing levels of Co2 (Hawaii) The famous evidence is from Mauna Loa Curve where a series of readings are taken at regular intervals of Co2 concentration on hourly basis. Air in the surrounding is free from local pollutants; hence it is a good representative of Northern hemisphere. Measurement started in 1958 while monitoring methods and instruments used have remained the same. Records show that the level of atmospheric Co2 has increased from 315.989 ppmv (parts per million by volume of dry air) in 1959 to 381.71 in 2006.

NB: Annual fluctuation in the levels of Co2 seems to be the results of seasonal differences in fixation of Co2 by plants.

HOW RELIABLE ARE DENDROCHRONOLOGY / PEAT BOG ESTIMATES OF AGE Both dendrochronology and peat bog dating are used to confirm radio-active dating in a process called wiggle matching. - Wood of known ages from ancient trees / or samples of peat bog are dated from radio carbon measurements and the result compared to give a form of calibration. This data can be used to determine the accuracy of their estimation of age, hence the data becomes more reliable. EFFECTS OF GLOBAL WARMING Assuming that the data models are reasonably accurate the following is likely is to take place:(a) Risk of flooding: The Antarctic temperatures have increased by 2.50c in the last 50 years, and 500 billion tones of ice have melted into the sea. The volume of water in seas and oceans will increase causing sea-level to rise. The volume of water in seas and oceans will increase causing sea-level to rise. As the water becomes warmer, the volume increases resulting in a bigger impact on sea levels. About 100 million people live less that1m above the current sea and hence are in danger, while countries like Netherlands may disappear. (b) Climate change: Rising temperatures affect weather and rainfall patterns e.g if the current trend of low rainfall continues, then by 2020 about 75 250 million people will have water shortage for crops and domestic use. (c) Effects on organisms: The metabolic reactions in organisms are enzyme controlled and have optimum temperature where they work best. Beyond this temperature, enzymes begin to denature and the rate of reactions falls. This could have effects on processes such as:(i) Rate of growth

If plants grow faster, there will be more uptake of Co2, thus reducing Co2 levels, while in other places organisms may die if denaturation takes place (if organisms are ectotherms I.e cold blooded). (ii) Reproduction e.g - In tropics insects which are pollinators are vulnerable, hence are likely to die therefore the plants and animals which feed on the plants may die. - In higher latitudes, seasonal cycles affect life cycles e.g warmer temperatures means plant grow and flower earlier. Insects such as moths and butterflies becomes active earlier in the warmth and plant food needed for caterpillars is available. - Bird e.g great tits are able to adapt by laying eggs 2 weeks earlier than 50 years ago. Thus breeding time is getting even earlier every year, but the caterpillars are emerging even earlier than birds and hence the latter are missing the peak population, thus raising fewer chicks. - In reptiles e.g crocodiles, the males develop if the eggs are incubated at 32-330c. If the temperatures are warmer or cooler, females develop thus global warming means only female crocodiles and hence end of species. (d) Changes in species distribution. Plants like alpines in mountainous part of UK are becoming rarer. As the environment becomes warmer, some animals are able to extend their ranges northwards and becoming extinct at the southern end e.g by 1999 the 35 species of non-migratory European butterflies 63% had shifted northwards and 3% to south. As the cold areas became warmer, disease carrying organisms like mosquitoes, ticks, rats will get ideal conditions hence there are likely to be a major increase in insect-borne diseases in Britain and Europe. As such the WHO has warned, hence the need to plan for preventive measures.

IMPORTANCE OF GREEN HOUSE GASES DATA The data on green house gases can be extrapolated i.e (the use of available data on which to base estimation of values which fall outside the known range) to make predictions on temperature in future as well as their long term effects. Predictions help plan international response to problems of rising Co2 levels and global warming.

NB: Limitations of extrapolations: It is impossible to tell the exact impact of Co2 on global warming. Impossible to predict impact of global warming on particular aspects of world climate.

Extrapolations do not take into account unknown factors in future e.g technology may change, current trends etc.

LIMITATIONS OF AVOIDING GLOBAL WARMING The scientists rarely agree on scientific views in any area e.g many agree Co2 levels including human emissions bring about global warming but others have different views. Politicians whose decisions are influenced by:(i) Political perspective e.g they tend to make unpopular policies with voters but good for the environment popular i.e reducing of fossil fuel prices means more vehicles more pollution. (ii) Pressure groups and lobbyists who are biased by their own interest.

Industrialists especially in the field of electricity generation, petrochemical industries etc have vested interests in promoting alternative theories for global warming to avoid legislation that changes their industry. WHAT NEEDS TO BE DONE IN FUTURE 1. Controlling the use of fossil fuels. 2. Making industrial processes and car engines cleaner and less polluting (reduction in emissions %). 3. Use of biofuels to replace fossil fuels. NB: According to carbon cycle, plants use Co2 during photosynthesis and release it when they are burned as fuels hence net gain or loss of Co2 in the atmosphere. - Land needed to grow the plants could threaten food production around the world leading to starvation for millions of people. 1. Use of alternative sources of energy e.g wind, solar, nuclear power although they have their own problems. 2. Use of waste plant materials e.g straw or wood pulp from paper making as raw materials for biofuels this would reduce the use of fossil fuels without taking crops space. 3. Reafforestation i.e re-planting of trees to replace the ones that have been lost, this removes Co2 from the atmosphere.

CAUSAL AND CORRELATION RELATIONSHIPS Causal relationship is where one factor directly causes effect e.g initially human activities like burning of fossil fuels in industries and vehicles increases Co2. Some scientists have proposed a mechanism where solar activity affects (prevents) clouds formation and hence surface temperature (falls).

However, according to IPCC (inter-governmental panel for climate change) they have reached the conclusion that some of these activities would most likely have produced cooling than warming effect. From increased studies on global warming e.g polar ice melting, climate change all are suggesting that, it is the increase in atmospheric Co2 that surface temperature increases. Thus, IPCC believe Co2 is the main factor hence, it is a causal link.

Correlation is a factor that appears to be linked to a change or event e.g both increase and decrease at the same time. Evidence from many studies suggests a clear correlation between increase in temperature and Co2 levels. However, the problem is that the correlation is too close to know whether increase in green house gases are causing increase in temperatures or rise in green house gases is the result of rising temperatures. SPECIATION AND EVOLUTION Terms used:(1) (2) (3) (4) Genome this is the term used to refer to all the DNA of the individual. Proteome this refers to all the proteins produced from DNA in an individual. Proteomics it is the study of different proteins and how they come about. Mutations these are sudden changes that occur on the genetic material and they can be inherited e.g (a) gene or point mutations where changes occur in a single base pair like deletion. (b) Chromosome mutation which involves the whole chromosome e.g translocation. Gene pool this refers to the total number of genes in a given population in a given area e.g selective breeding of brassica oleracea shows a huge amount of genetic variety in that gene pool. Pg 54 Allele this is the alternative form in which a gene expresses itself e.g the gene for skin colour can express itself as brown or dark. Allele frequency it is the relative occurrence / frequency of a particular allele in a population. Evolution it refers to a change in the allele frequency or is a process by which species of living organisms undergo permanent change as a result of natural selection in response to a change in their environment. Gene families these are groups of closely related genes e.g the genes which code for globin and globin molecules which have sight differences in amino acids chains. Different members thus express themselves as haemoglobin, myoglobin, foetal haemoglobin etc.

(5) (6) (7) (8) (9)

How evolution can come about through gene mutation and natural selection

The sequence of organic basis on the DNA that codes for adult haemoglobin is as shown below:Nucleotide CTG ACT CCT GAG GAG AAG TCT

Amino acids -

Leu Thr Pro Glu Glu Lys - Ser

Due to mutation which is substitution, the sequence of the organic basis has changed thus the mutant adult haemoglobin (HBS) is as follows:Nucleotide CTG ACT CCT GTG GAG AAG TCT

Amino acids Leu Thr Pro Val Glu Lys - Ser This mutation causes sickle cell anaemia whereby, the RBC is sickle shaped, and is less efficient in carrying oxygen and move likely to clog up in the blood vessels especially capillaries. Sickle cell anaemia expresses itself under homozygous recessive conditions and it can be removed from the gene pool through death before the homozygous individual can reproduce. Heterozygous individuals have mild anaemia but usually remain well. However, if infected by malaria parasites, those sickle cells RBC are removed by the spleen together with the parasites. Hence, the heterozygous individual confers some resistance to malaria, and there is a natural selection for people who are heterozygous in malaria regions and the allele frequency is higher than normal.

SPECIATION This is the process by which species are formed from a population and there are 2 main ways:(i) Allopatric speciation where populations are separated by geographical barriers (ii) Sympatric speciation where populations are reproductively isolated. Describe how apple maggots can be described as a new species emerging A tiny fruit-fly (Rhagoletis pamonella) lived on hawthorn bushes laying their eggs on the fruit, where they developed to maturity (this was in Hudson river valley in USA) Adult fruit-fly responds to hawthorn smell and return to reproduce. Some apple orchards genetically closely related to hawthorn were planted and some fruit-flies laid their eggs on the apples by mistake or for not seeing hawthorn. The larvae did not do well as most died and a few were left which responded to smell of apples when mature, and therefore formed apple dwelling flies (evolved).

The two populations show increasing reproductive isolation as they mate with flies on the same food source. Apples provide more food and better protection for maggots from parasitic wasps. Upon analyses, the allele frequency in the flies is becoming increasingly different. It seems that2 entirely different species will evolve which will no longer interbreed, as their reproductive cycles are out of phase i.e not synchronised.

REPRODUCTIVE ISOLATION Reproductive isolation occurs when:(i) Fertilization is prevented (1) (Pre-zygotic barriers) in the following ways:(a) Habitat isolation the populations select different habitats in the same area and thus do not come into contact during the reproductive season e.g tiny fruit-flies. (b) Temporal isolation most organisms have brief mating or flowering periods (hours or days). If the 2 populations get out os synchronization they cannot mate with each other. (c) Mechanical isolation mutations may result in a physical barrier for fertilization e.g position of the sex-organs cannot allow mating to take place. (d) Behavioural isolation if the behaviour of animals changes, they may not recognize other members of the same species as mating partners e.g dancing in birds. (e) Gametric isolation when female gametes fail to attract a male gamete / or male gamete cannot penetrate the female gamete, then the individuals which produce the gametes cannot interbreed e.g in plants, pollens of one species cannot form an effective pollen tube on the stigma of another species. (ii) Post zygotic barriers (a) Low hybrid zygote vigour the zygote fails to develop properly and die during embryonic development / or results in offsprings with severe abnormalities thus cannot reproduce successfully. (b) Low hybrid adult viability off-springs fail to thrive and grow properly. (c) Hybrid infertility off-springs may appear healthy but are infertile e.g mule DNA PROFILING This is the observation made at the non-coding areas of DNA to identify patterns which are unique to individuals but which can be used to identify relationships between individuals and even species. Role of the scientific community in validating new evidence by DNA profiling:-

(a) The red deer stags that live in woods and parklands have antlers much bigger and broader than stags that roam highland mountain sides, thus they could be easily mistaken for different species yet DNA evidence shows that they are the same. (b) Molecular geneticists, in trying to help plant breeders and disease control specialists have DNA evidence based on genes and proteomics that there are Atleast 8 different species of fusarium pathogens which have similar effects on crop plants. (c) The caviar is a luxury food, but he most expensive is beluga caviar from beluga sturgeon (eggs). DNA profiling for different tins of caviar showed that 25% thought to be beluga caviar contained eggs of other less prestigious species. (d) Fossil DNA and human evolution human evolution is difficult to follow due to limited fossils evidence, but now by extracting DNA from fossils under 100,000 years and letting it undergo polymerase chain reaction (PCR) (amplifying). - It was thought that Neanderthals who lived 30,000 to 100,000 yeas ago were ancestors of modern humans. - By comparing DNA from Neonderthals fossils with DNA of modern humans have shown that Neonderthals were not our ancestors and inter-breeding between Neonderthals and modern human ancestors is unlikely to have taken place. (e) DNA, lice and human evolution - Modern humans have 3 types of lice i.e head lice, pubic lice and body lice. - Body lice hang on clothes but feed on the body. - DNA evidence suggests common ancestors of humans and chimpanzee which diverged 6m years ago as well as the head lice species. - DNA analyses shows head lice and body lice formed separate species around 72,000 years ago when woven clothing became common. - DNA profiling show pubic lice are more closely related to gorilla lice than other human lice. - Thus, humans and gorilla had the same ancestors but diverged about 6m years ago while pubic and gorilla lice diverged 3m years ago. - Overall DNA evidence is that human had head lice with chimpanzee lice ancestors and pubic lice with gorilla lice ancestors. (f) New models support old theory - DNA analyses of many species help build diagrams that model the evolution of species from a common ancestor e.g in primate evolution by using fossil evidence and morphology. There are three main families:(i) Hylobatidae (gibbons) (ii) Pongidae (gorillas, chimpanzees, orang-utans) (iii) Homidae (humans) Using DNA fossil analysis, there are 2 main families, 2 sub-families and 3 tribes. Family 1. Hylobatidae Ponginae Sub-family Tribe examples Gibbons Orang-utans

2. Hominidae Garillini Hominae Panini Homini IMPORTANCE OF DNA Genetic code: A protein is determined by the specific arrangement of amino acids. The order of the nucleotide bases in the DNA determines the order in which amino acids are arranged in a protein. This relationship between the DNA nucleotide bases and amino acids is known as the genetic code. FEATURES OF A GENETIC CODE (a) Three organic bases in a sequence, code for a particular amino acids and are referred to as triplet or codon. (b) All codons are universal i.e they are similar in all organisms. (c) Some triplets / codons e.g UAA, UAG, UGA do not code for any amino acids and are called stop or non-sense codons. (d) Some amino acids have more than one triplet e.g Arginine has CGU, CGC, CGA, CGG and AGA. For this reason, the code is said to degenerate. (e) The code is non-overlapping i.e each triplet is read separately e.g CUGAGCUAG is read as CUG-AGC-UAG and not CUG-UGA-GAG-AGC etc PROTEIN SYNTHESIS The body has different types of proteins e.g enzymes, hormones, antibodies, haemoglobin etc. Each of these proteins has its own code within the DNA molecule. The section which has the code is referred to as the gene or the cistron. Two main processes are involved:1. Transcription: This is the process by which a complementary MRNA is formed using DNA as a template / coding strand / antisense strand (5-3). It takes place in the nucleus of the cell. The DNA molecule unwinds by breaking of hydrogen bonds using DNA helicase. The RNA polymerase (DNA-directed RNA polymerase) becomes attached to the double helix of DNA at a codon for the amino acid methionine whichacts as start signal. Gorillas Chimpanzee Humans

The bases on the DNA become exposed and they attract the complimentary e.g C attracts G, A attracts U etc The RNA polymerase then joins the nucleotides to form a M-RNA strand. Guanine (G) is added to 5 of the MRNA and is referred to as Cap a signal for promoting translation. At the end of 3, a tail of approximately 100 adenines nucleotides are added called poly-A a signal for the export of MRNA from the nucleus as well as protection from enzymes. M-RNA contains non-coding regions called introns and coding regions called extrons. Thus, introns are removed by enzyme action. Function of introns is not known. The MRNA then leaves the nucleus through the n. pore to the cytoplasm where translation takes place. The DNA now zips up with the help of DNA polymerase.

TRANSLATION It is the process by which the sequences of the organic bases are converted into a sequence of amino acids in a protein. Ribosomes attach onto the MRNA with the small sub-unit on the lower scale and the large sub-unit on the upper side. The ribosome encloses two codons at a time. The complimentary bases of a codon are referred to as anticodons which are found on the transfer RNA, whose terminal end carries with it a specific amino acid. The anticodons on the t-RNA are attracted by the codons on the M-RNA and they are joined by hydrogen bonds.

NB: The enzyme transferase, transfers the t-RNA onto the M-RNA. The same process is repeated by the 2nd t-RNA which carries the second amino acid. The first peptide bond is formed between the first and second amino acid by condensation reaction to form a dipeptide. The hydrogen bonds between the codon and the anticodon of the 1st t-RNA are broken, releasing the t-RNA back to the cytoplasm leaving the amino behind. In the cytoplasm, the released t-RNA combines with its specific amino acid with the help of amino acyl t-RNA synthetase. The ribosome moves enclosing the 3rd codon and the same procedure is followed until the ribosome reaches the stop / non-sense codon i.e UAA UGA, AUG etc where protein synthesis stops. Hence, a molecule of protein (polypeptide) is formed. If several molecules are required, then several ribosomes pass over the MRNA, each making a polypeptide.

The formed proteins are taken to the golgi body for modification e.g they could be converted into tertiary, quaternary structure or carbohydrate can be added to form glycoproteins.

How one gene can give rise to more than one protein through post-transcriptional changes to M-RNA The RNA transcribed from DNA is called pre-MRNA. It contains non-coding areas called introns and coding areas referred to as extrons. Thus, when first transcribed, it is not quite finished. The ends are capped 5 with guanine, 3 poly A. The introns are removed by a process called RNA-splicing when enzyme complexes called spliceosomes are involved. Sometimes some extons are removed as well thus the code on the final MRNA is different from the code on the DNA. Hence, polypeptide chains are with slight differences in amino acids formed which in turn produce different proteins. Thus, post-transcriptional changes lead to a variety in the phenotype than is coded for directly in the genotype e.g human DNA contains 25,000 genes but codes for more than 90,000 different proteins.

MINI-SATELLITES AND MICRO-SATELLITES Micro-satellites are sections of DNA molecule with 20-50 bases and repeated from 50 to several hundred times, while mini-satellites are sections of a DNA with 2 4 bases repeated between 5 and 15 times. NB: Mini or micro satellites appear in same positions on each pair of homologous chromosomes but the numbers of repeats vary depending on patterns inherited from parents. DNA profiling and its use for identification & determining genetic relationships between organisms The DNA molecule is separated from the sample. It is broken down into fragments using restriction endonucleases at particular points in intron sequences referred to as recognition sites. Restriction enzymes cut mini and micro satellites, sequences such that they remain intact, thus giving a mixture of them. The fragments are separated and identified in a process called gel-electrophoresis. The DNA fragments are placed in wells in an agarose gel medium in a buffering solution (to maintain a constant PH).

The gel contains a dye (e.g ethidium bromide) which binds onto the DNA fragments on the gel. The dye fluoresce when placed under U.V light (responsible or DNA bands). A dye is also added to the DNA sample which does not bind with DNA, but moves through the gel slightly faster than the DNA so that the current can be turned off before all the samples run off the end. An electric current is passed through the apparatus and DNA-fragments move towards the positive anode (due to the ve charge on the phosphate group in the DNA). Fragments move at different rates depending on mass and charge. When electrophoresis is over the plate is placed under U.V light and the DNA fluoresces and shows up. Southern blotting is then done, whereby an alkaline buffer solution is added to gel after electrophoresis and a nylon filter or nitrocellulose added placed over it. NB: Alkaline solution denatures the DNA fragments so that the strands separate and base sequences are exposed. Dry absorbent paper is used to draw the solution containing the DNA fragments from gel to the filter, leaving the DNA fragments as blots on the filter. Radioactive single stranded DNA probes (gene probes) are used to bind to specific portions of the fragments known as the core (target) sequences. Portions of the DNA not bound (hybridizing) to the radioactive probes are washed off. The remaining DNA still attached to the nylon membrane is placed next to a sheet of x-ray film. The radioactive probes on this DNA expose the film revealing a pattern of light and dark bands, and when developed, the pattern makes up genetic fingerprint. DNA AMPLIFICATION USING POLYMERASE CHAIN REACTION (PCR) PCR adapts the natural process in which DNA is replicated in cells, thus making enough DNA for profiling from tiny traces. The following are required:(a) DNA sample to be amplified. (b) DNA polymerase (c) Primers I.e small sequences of DNA which join to separated DNA stands. (d) Good supply of the four nucleotide bases i.e G, C, A and T.

All these are mixed together in PCR machine. The mixture is heated to 930c in order to separate the strands by breaking the hydrogen bonds. The mixture is then cooled to 550c so that primers join / anneal / bind to the single stranded DNA by hydrogen bonds to complementary portion of the DNA. NB: Primers are normally in excess.

It is then heated to 750c optimum temperature for DNA polymerase to build up a complimentary copy of each DNA strand, thus restoring double structure of the DNA. The cycle is repeated each time; the DNA copied becoming the template.

STRUCTURE OF A GENERALISED BACTERIUM

Slimy capsule: It is formed from starch gelatin, protein or glycolipid. It helps the bacteria to attach onto surfaces e.g intestinal walls, teeth etc

Prevents bacteria from desiccation. Prevents it from being destroyed by chemicals or other cells e.g WBC by phagocytosis. Helps bacteria to form colonies. It covers the cell markers (receptors) which identify the cell, hence are pathogenic as cannot be identified by the hosts immune system e.g pneumonia, TB, meningitis etc.

Cell wall: It is made up of peptidoglycans / mucopeptides / or murein (which are composed of hexose + amino acids). Bacterial cells are hypertonic hence water moves in by osmosis, the cell wall prevents swelling and bursting of the cell. It protects bacteria from lysis e.g by certain chemicals e.g antibiotics. Helps in forming the shape in bacteria. Cell membrane: It is a lipid-bilayer The protein molecules are higher than in eukaryotic cells. It allows substances to move in and out. It secretes enzymes and toxins to the outside environment. They fold inwardly increasing surface area (mesosomes) for metabolic reactions such as respiration and photosynthesis. It is involved in the cell wall synthesis during cell division. Granules: They include glycogen, lipids PHB (polyhydroxybotyric acid) which are sources of energy when required. Ribosomes: It is the site for protein synthesis Plasmids: They are small loops of DNA molecules with a few genes for:- (1) Growth (2) Production of toxins or resistance to a particular antibiotic. - They are involved in genetic engineering. Bacteria chromosome / circular DNA: This is otherwise referred to as the nuclear material. It contains the DNA and is not surrounded by a nuclear membrane. Flagella:

They are made from proteins called flagellin (not microtubules). It moves the bacteria by rapid rotations about 100 revolutions per second.

Pili / Fimbriae: These are projections from the cell membrane through the cell wall. They are concerned with attachment to other bacteria or host cells. The fimbriae are short and bristle like and therefore prevent phagocytosis by WBC. The pili are long and numerous, and are associated with process of conjugation. Pili make bacteria vulnerable to viral infections while bacteriophaes can use them as entry points. CLASSIFICATION OF BACTERIA (a) Shape: Rod shaped are referred to as bacilli. Spherical shaped are referred to as cocci which include:Diplococci staphylococcus streptococcus

Spiral or twisted which are referred to as spirila. Vibrio i.e comma-shaped bacteia like those which cause cholera.

(b) Respiratory requirements e.g: Obligate aerobes need oxygen for respiration. Facultative anaerobes use oxygen if available but can manage without. Obligate anaerobes respire in absence of oxygen (c) Gram stain: Prepare a heat fixed smear for e.g yoghurt, milk etc. Add crystal violet on the microscope slide. All the bacteria take up the strain. The slide is then flooded with grams iodine which intensifies the crystal violet by making it form crystals. The slide is then rinsed in alcohol. Bacteria with thick cell wall retain the crystal violet which does not get washed out when alcohol is added and they appear purple (this is due to teichoic acid on to which the stain binds and resists decolouration). Thus they are referred to as gram +ve. Bacteria with a thin cell wall do not retain any colour as it is washed out by alcohol and are referred to as gram ve (since they dont have teichoic acid). However, counterstaining with safranin makes appear pink or red 9those which were gram ve) The gram +ve remain purple.

REPRODUCTION IN BACTERIA There are two main ways:(a) Asexual reproduction by a process called binary fission: The DNA is replicated and the old cell begins to breakdown round the middle of the cell. The DNA is held in position by mesosomes. Enzymes break open the circular piece of DNA allowing strands to unwind and be replicated. New cross-walls are laid down between the two daughter cells. New cell membrane and cell wall materials extend inwards forming a septum i.e partition. This divides into 2 daughter cells. Plasmid also divides.

NB: The time between cell division is known as generation time which can be around 20 minutes depending on the environmental factors. A bacterium divided by binary fission after every 20 minutes. What would be the population of bacteria after 3hrs? pg space (b) Sexual reproduction: This involves the transfer of genetic material from one bacterium to another by:(i) Transformation: This is when a short piece of DNA is released by a donor and actively taken up by a recipient where it replaces a similar piece of DNA. (ii) Transduction: When a small amount of DNA is transferred from one bacterium to another by a bacteriophage, this small amounts of DNA become incorporated into the host DNA. (iii) Conjugation: This takes place when the bacterias are in direct contact. The donor (F+) equivalent to a male produces a sex pilus a cytoplasmic bridge between the two cells, through which DNA is transferred to the recipient cell (F-). EVIDENCE FOR TRANSFORMATION

This was done using two forms of pneumocococcus i.e rough type R which had no capsule and did not cause the disease and smooth type S which had a capsule and caused pneumonia.

R-type Non-virulent

S-type virulent

heat killed S-type

R-type and heat killed S-type

Rat

rat

rat

rat

Lives

dies

lives

dies

Those mouse that received live R bacteria and dead S bacteria developed pneumonia and died a few days later, and S-type bacteria were isolated from its blood. Conclusion was that, living R-cells had taken up a factor from the dead cells which transformed the R-cells into S-cells thus developing a capsule and resists attack by host cell and cause the disease.

MICRO-ORGANISMS AND DECOMPOSITION OF ORGANIC MATTER The decomposers (saprophytes) secrets enzymes which digest the dead organic matter (extra-cellular digestion). The digested material e.g glucose diffuses into the decomposers where they undergo respiration releasing simple inorganic molecules e.g Co2, water etc. They convert dead bodies into ammonium compounds, then nitrites, and finally into nitrates which return to the soil in the nitrogen cycle. Nitrates provide nitrogen required in the formation of amino acids, which in turn make proteins for growth in organism. M/o ensures recycling of mineral salts. They prevent piling of dead bodies of organisms. In the carbon cycle, the M/o produce the enzyme cellulose which breaks down cellulose from the plant cell walls to give sugars which can be used as food (source of energy) by a variety of other M/o.

M/o such as bacteria and fungi releases about 25 x 1012kg of carbon per year into the atmosphere compared to 6 7 x 1012kg per year by burning of fossil fuels.

PATHOGENS These are disease causing organisms by: Producing poisonous substances toxin Damaging the tissue directly When natural flora get out of control i.e becoming pathogenic

NB: Bacteria (pathogenic) produces:(a) Exotoxins which are soluble compounds secreted by the cell into the immediate environment and they are required in small quantities to give rise to symptoms in the host e.g staphylococcus. (b) Endotoxins these are toxins which are released from the bacteria when the cell wall is damaged or when lysis occurs. They are required in large amount to have any symptoms e.g salmonella. Food poisoning caused by staphylococcus may result to vomiting and diarrhoea between 1 6 hours, after ingestion of the exotoxin. If caused by salmonella (endotoxin) vomiting and diarrhoea may start 1 2 days later. The five main groups of pathogens are:(i) Viruses (ii) Bacteria (iii) Fungi (iv) Protoctists e.g amoeba, plasmodium etc (v) Metazoa i.e worms e.g round worms, tape worms etc VIRUSES: They are the smallest of all M/o, and they range from 0.02 to 0.3 m across i.e diameter. They are not cells and they require living cells in order to reproduce. NB: They are referred to as living things as they can reproduce and change in adaptive ways. General structure of a virus

They contain a core of nucleic acid either DNA or RNA. They are surrounded by a protein coat known as the capsid made up of small units known as capsomeres. Capsid has the following functions:(i) it protects the nucleic acids of virus from enzymes and chemicals when outside the host cell. (ii) It helps the virus to attach on to the host cell. The envelope contains the receptor site which the virus uses to attach on to the host cell. Lipid envelope makes it easier for the virus to pass from cell to cell. VIRUS SHAPES They have a variety of shapes e.g (a) Helical e.g tobacco mosaic virus which is composed of rod shaped capsomeres which are attached onto the RNA which is coiled. The RNA is a single stranded nucleic acid. pg photocopy (b) Polyhedrons e.g (i) H.I.V (Human Immunodeficiency Virus) (ii) Herpes virus (STD)

 The capsid is usually many sided, whose faces are either triangular or circular and the nucleic acid is packed at the centre. (c) Complex e.g bacteriophage T2 They have a polyhedral head and helical tail as in phage such as bacteriophage ( a virus that destroys bacteria). The phage consists of a head with a double strand DNA wrapped around a core of protein surrounded by a polyhedral capsid and a helical tail. Photocopy pg NB: Viruses attach to host cells by means of specific proteins antigens called viruses attachment particles (VAPs) which target proteins in the host C.S.M. - Viruses are transmitted through:(i) Droplet inhalation during sneezing, coughing etc (ii) Contaminated food or water (iii) Through insect bites e.g aphids (iv) Sexual transmission (v) Blood transfusion (vi) Through placenta or during breast feed to babies - The viruses enter into a cell in 3 main ways as shown below pg photocopy LYTIC AND LYSOGENIC PATHWAYS Once inside the host cell, the capsid is shed and the nucleic acid is released. The viral MRNA is formed and the host cells ribosomes are used to synthesize viral protein molecules. The new viral nucleic acid is replicated in the nucleus of the host cell. The virus proteins are assembled with the capsids forming around the nucleic acid, in the cytoplasm of the host cell. An enzyme lysozyme is synthesized or released which breaks down the C.S.M releasing the viruses. This is referred to as lytic cycle or pathway and the virus is said to be virulent i.e disease causing. NB: When the viruses are released by budding, they have a cell membrane from the host cell surrounding them, and in this process the host cell is not destroyed. In latent pathway (cycle) the viral genetic material becomes incorporated in the genome of the host cell. Thus, the DNA is replicated every time the host cell divides.

This inserted DNA is called provirus, and MRNA is not produced from the viral DNA as one of the viral genes causes the production of a repressor protein which makes it impossible to translate the rest of the genetic material. Photocopy pg

LIFE CYCLE OF A RETROVIRUS Retroviruses are viruses which contain:(i) RNA as the nucleic acid. (ii) An enzyme called reverse transcriptase e.g HIV The retrovirus attacks an animal cell via some receptors sites that are specific e.g gp41 in HIV and CD4 on WBC. The viral RNA enters the host cell, but cannot be used as MRNA. The viral RNA is converted into viral DNA by the enzyme reverse transcriptase. The viral DNA is incorporated into the host DNA in the nucleus, and directs the production of new viral genome RNA, MRNA and coat proteins. New viral particles are assembled and leave the host cell by exocytosis. Viral DNA remains in the nucleus and so the process is repeated. Pg 85 fig 6.2.4 VIRUSES AND DISEASES They cause diseases in animals, plants and bacterias. They cause lysis of cells of the host by making them release their own lysosomes and digest them from inside or by production of toxins that inhibits cell metabolism. Some particular tissues are affected by viruses e.g adenoviruses which cause colds affects respiratory tissues. This specificity is due to presence or absence of cell markers on the surface of the host cells e.g Angiosperms (flowering plants) are vulnerable to viral diseases but gymsosperms (conifers) are not. Diseases caused by viruses include flu, measles, AIDs, cancer etc

ROUTES PATHOGENS MAY TAKE WHEN ENTERING THE BODY Most infections are communicable i.e the infection is capable of spreading from one person to another. Pathogens can be transmitted on different ways:(1) Body openings e.g eyes, nose, mouth, ears, anus, urinogental openings etc. (2) Vectors these are the organisms which transmit the disease causing organisms e.g mosquitoes transmit plasmodium which causes malaria.

(3) Formites these are inanimate objects that carry pathogens from a host to another e.g hospital towel, beddings, under wears which may transmit staphylococcus infections. (4) Direct contact this is mainly the case for skin diseases especially in children. Most sexual diseases are also spread by direct contact of genital organs e.g gonorrhoea, syphilis etc. (5) Inhalation when one coughs, sneezes or talks, many droplets are expelled from the respiratory tract. - Part of the water in droplets evaporates leaving very tiny droplets full of pathogens and remains suspended in the air for a long time. - When they are inhaled, they gain entry to a new respiratory tract, starting of another infection e.g influenza, measles, tuberculosis etc (6) Ingestion pathogens causing gut diseases are transmitted by contaminated food or drinks especially raw or undercooked food e.g diarrhoea, Hepatitis A, salmonelle poisoning etc (7) Innoculation a pathogen can be inoculated into the body directly through injured skin from contaminated medical instruments or sharing needles e.g for drug abuse. - An infected animal may bite, lick or scratch. - Contaminated knives, thorns, stones may inoculate M/o which cause tetanus, HIV, Hepatitis B etc. ROLE OF BARRIERS IN PROTECTING THE BODY FROM INFECTION The body has natural barriers i.e (a) Epithelial defences: (i) Skin it is an impermeable layer toughened by keratin, a fibrous structural protein which forms a physical barrier between the environment and the inside delicate body tissues. - The skin produces an oily substance called sebum from sebaceous glands, which contain a chemical that inhibits growth of M/o, but not the natural ones which are adapted for survival on skin surface. (ii) Surfaces of internal tubes e.g respiratory system gut, urinary and reproductive tracts. - They produce defensive secretions e.g mucus which traps M/os. - Mucus contains lysozymes i.e enzymes capable of destroying microbial cell walls, especially gram +ve. - Lysozymes are also present in tears etc. - Cilia beat rhythmically moving mucus in oviducts. - Phagocytic WBC which engulf and digest pathogens are often present on the epithelial surfaces. NB: Skin cuts may allow M/o such as herpes, viruses, meanwhile bites from hookworms, ticks, insects may introduce M/o, but this is counter acted by process of blood clotting.

(b) In the gut: Saliva has bactericidal properties e.g some polypeptides produced in salivary glands destroy bacteria. HCL in the stomach with PH2 destroys most of ingested M/o. The natural flora in the gut usually competes for nutrients and space with any M/o which manages to reach the stomach. By vomiting i.e when the contents of the stomach are forcibly discharged out of the body through mouth. This could be due to toxin, bad smell, pregnancy and tumours.

NON-SPECIFIC RESPONSES OF THE BODY TO INFECTIONS Non-specific responses refers to the ability of the body to recognize the differences between self (your own cells) and non-self (a foreign cell or organism that gets into your body) and reacts against anything that is no-self. There are various ways:(a) Inflammation: It is a non-specific way in which our bodies respond to infection. It involves mast cells found in connective tissue below the skin and in blood vessels. When the tissues are damaged, mast cells as well as damaged WBC release chemical called histamines. It causes arterioles to dilate, causing local heat and redness. The locally raised temperatures reduce the effectiveness of pathogens reproduction in the area. It also makes capillaries leaky, thus a liquid containing plasma, white B.C and antibodies are forced out of capillaries causing swelling (oedema) and pain. They destroy and disable the pathogens. NB: Fever is the early non-specific response to infection by the body, where the hypothalamus is stimulated to reset the body to a higher temperature. - Importance of fever is that:(i) Most pathogens reproduce quickly at 370c or lower, thus this reduces the reproduction rate, causing less damage. (ii) The specific response system works better at higher temperatures, by combating infection. High temperatures above 400c may cause denaturation and may lead to permanent tissue damage. (b) Phagocytosis:

It involves 2 types of WBC i.e (i) (ii) Granulocytes which have granules e.g neutrophils which make up about 70% of WBC the lobed nucleus ensures that they are able to squeeze through cells e.g blood capillaries. Agranulocytes i.e without granules e.g macrophage that make up 4% of WBC. - During phagocytosis, WBC engulf and digest pathogens or any foreign material. - Dead neutraphils form pus which ooze out of a wound or may be reabsorbed by the body.

(c) Lysozyme: This is an enzyme present in tears, mucus and other body fluids. The destroy bacteria by disrupting the bacterial cell wall. (d) Interferons: When cells are invaded by viruses, they produce a group of chemicals called interferons. They prevent viral replication within the cell. The interferon diffuses from the cells making them, to the surrounding cells and binds onto the receptors in the surface membrane of uninfected cells. This stimulates a pathway which makes the cells resistant to infection by virus thus preventing their reproduction. NB: An antigen is a substance that stimulates the production of an antibody when it gets into the body. They are chemicals on the surface of a cell e.g proteins, glycoproteins or carbohydrates. They can be toxins made by bacteria or at times are whole micro-organisms e.g bacteria or viruses.

IMMUNE SYSTEM This is the specific response of the body which recognizes and destroys foreign cells. NB: Each organism carries its own unique set of markers or antigens on the cell surface membrane. Some markers are common to members of a particular species, others to a particular individual etc. TYPES OF WBC INVOLVED IN THE IMMUNE SYSTEM

(a) Lymphocytes these are agranulocytes made in the white bone marrow of the long bones. They move around the body in blood, lymph and recognizes as well as responding to foreign antigens. (b) Macrophages these are agranulocytes which have left the blood stream and move freely through the tissue. CHARACTERISTICS OF THE IMMUNE SYSTEM (a) (b) (c) (d) It can distinguish self from non-self. It is specific i.e it responds to specific foreign cells. It is diverse i.e can recognize an estimated 10 million different antigens. It has immunological memory i.e once it has met and responded to a pathogen, it can respond rapidly if it meets it again.

TYPES OF LYMPHOCYTES INVOLVED IN THE IMMUNE SYSTEM (a) B-cells: They are made in bone marrow (where stem cell are). Found in lymph glands and free in the body. They have membrane bound globular receptor proteins, identical to antibodies they produce later. All antibodies are called immuno-globulins, while membrane bound antibodies are known as IgM. As an embryo grows about 100 million B-cells are formed each with a different membrane bound antibody. Each then divided to form a clone of cells. Thus, the babys immune system has the potential to recognize and tackle a variety of pathogens.

(b) T-cells: They are made in the bone marrow, but mature and become active in thymus gland. The surface of each T-cell has thousands of identical T-cell receptors. There are two main types of T-cells:(i) T-killer which produce chemicals that destroy pathogens. (ii) T-helper which produce antibodies against the antigens on a particular pathogen. NB: The working process of most of these cells depend on special proteins known as major histocompatibility complex (MHC) proteins which displays antigens on the cell surface membrane.

THE HUMORAL RESPONSE The humoral response of the immune system consists of 2 main stages i.e Thelper activation and the effector stage. Pathogens enter the body and the non-specific response, rapidly brings them into contact with macrophage. They engulf them by phagocytosis forming vesicles. This then fuses with lysosomes, whose enzymes breakdown the pathogen and separate off the antigens. This is known as antigen-processing. The processed antigens combine with MHC proteins forming complexes and moves to the surface of the cell membrane. The macrophage with antigen /MHC protein complex on the surface of the cell membrane is known as antigen-presenting cell (APC). The T-helper cell has CD4 receptors on the outer membrane, which binds to the specific antigen of the antigen /MHC complex on the APC. This triggers the T-helper cell to reproduce and form a clone of cells. The new cells have the same CD4 receptors as the original T-helper cell, thus are specific for the original antigen. The cloned cells become:(i) Active T-helper cells used in the rest of the immune system. (ii) The remainder of the cloned cells become inactive T-memory cells, but become active if the same antigen is encountered again.

EFFECTOR STAGE B-cells and T-helper are active in the effector stage. Some of the B-cells will have immunoglobulins that are specific for the antigen presented by the pathogen and will bind to it. The B-cells then engulfs the whole pathogen by endocytosis. The vescle formed fuses with lysosome. Enzymes breakdown the antigen to leave fragments of processed antigen. They become attached to MHC/antigen complex and then transported to the cell surface membrane, where antigen is displayed, equivalent to another type of APC. A T-helper cell from the active clone recognizes the specific antigen displayed on the MHC complex on the B-cell and binds to it. This triggers the release of cytokines from T-helper cells which stimulates the Bcell to divide, forming identical clones i.e B-effector cells and B-memory cells. NB: The cloning of the B-cells results in the formation of correct antibodies to get rid off pathogens and this is known as clonal selection. The B-effector cells which are majority then differentiate into plasma cells clones. The plasma cells produce large amounts of antibodies. (An antibody is a special protein that is released into the circulation and binds to a specific antigen, on a particular pathogen that has triggered the immune system causing its destruction).

Each plasma cell secretes antibodies, identical to the immunoglobulin of the original parent B-cell. Plasma live for only a few days but can produce up to 2000 antibody molecules per second. NB: They have extensive R.E.R which is an adaptation for their role in producing large quantities of protein antibodies. The B-memory cells are long lived. They make the body to respond rapidly to a second invasion by the same antigen, as antibodies are formed and hence no symptoms are formed.

THE ROLE OF ANTIBODIES IN DEFENCE OF THE BODY AGAINST FOREIGN MATERIALS They reduce the ability of most pathogens to invade host cells when combined with antibodies. When pathogens / antigens are bound onto antibodies, the M/o agglutinate / clump together preventing their spread. The antigen-antibody complex is readily engulfed and digested by phagocytes. The antigen-antibody complex may stimulate other reactions e.g destruction of membrane of the antigen or the release of histamine by invaded cells causing inflammation.

CELL MEDIATED RESPONSE This is common to viral infections as they are inside host cell and the humoral response is not very effective. When a body cell is infected with a bacterium or a virus, it is digested and the antigens become bound to an MHC. The body cell thus becomes APC. The T-killer cells are exposed to cytokines from active T-helper cells; they undergo cell division producing clones of T-killer cells which binds on infected cells. The T-killer cells release enzymes that make pores appear in membrane of infected cells. This allows free entry of water and ions, the cell swells and bursts. Any pathogens which are released intact are labeled with antibodies produced by the B-effector cells and they are destroyed. Some cloned T-killer cells become T-killer memory cells so that a rapid response takes place if same pathogen attacks again.

INFECTIOUS DISEASES (a) Tuberculosis: It is caused by a bacterium called mycobacterium tuberculosis.

It is spread by droplet infection through coughing, sneezing, breathing etc in crowded conditions. People who are sick, malnourished or with problems of immune system are more vulnerable than healthy well fed people. It is also caused by mycobacterium bovis which affects cattle, through drinking infected milk or living in close contact with cattle. Areas of the body affected:

The bacterium affects the respiratory system by damaging lung tissues. Once inhaled into the body, they multiply slowly during primary infection, with no obvious symptoms. If one has a healthy immune system, there will be a localized inflammatory response forming a mass of tissue called a tubercule containing dead bacteria and macrophages (hence tuberculosis). Mycobacterium also target T-cells, reducing the production of antibodies. The bacteria are temperature sensitive and stop producing above 420c. However, human enzymes start to be denatured at around 400c, putting the patient at risk of dying before bacteria are inhibited.

NB: M.t. can avoid the immune system by producing a thick waxy outer layer which protects them from enzymes of macrophages. - The bacteria remain in tubercules, dormant or growing slowly until the person is malnourished or their immune system becomes weakened. - At this time they produce active tuberculosis. - In this way, the most effective bacteria are selected and passed on. EFFECTS OF MYCOBACTERIUM TUBERCULOSIS With active TB, bacteria multiply rapidly in the lungs. Symptoms include fever, night sweat, loss of appetite and loss of weight. Infections in the lungs causes cough, lung tissues become damaged and blood may be coughed up in the sputum. Alveoli breakdown, thus reducing surface area for gaseous exchange. Finally TB causes death as the individual cannot get enough O2 from the air as the lungs are damaged or Organs may fail due to lack of nutrition Since TB affects the immune system, sufferers become vulnerable to other opportunistic infections e.g pneumonia which may cause death.

HOW IS TB DIAGNOSED, CONTROLLED AND TREATED A chest x-ray will show TB damage to the lungs as apaque areas and large thick-walled cavities.

However, confirmatory tests can be done by examining the DNA of the bacteria, which gives immediate and reliable results. Controlling of the disease involves the following:(i) Improving living standards i.e less crowded housing and working conditions. (ii) If people remain healthy and better fed. (iii) Pasteurizing or heating milk before it is drunk, helps prevent mycobacterium bovis. (iv) Where disease is rare, people in contact with affected people are tested for TB and either immunized or treated. (v) Immunization through vaccination where the subjects are injected with live attenuated strain of mycobacterium. (vi) In UK this is done in babies as well as immigrants. Treatment involves different antibiotics for several months so that even resistant mycobacterium to some antibiotics will be destroyed together with rapidly producing bacteria, as well as those hidden in the cyst. This is followed by another 4 7 months taking of 2 antibiotics. By 9 months most patients are free of TB although it can take 12 18 months for all traces of active disease to disappear.

NB: The number of cases of TB are increasing due to:(i) (ii) (iii) (iv) Deteriorating social conditions in some areas. Immigration / and movement of refugees between countries. Intravenous drug use (as subjects share needles) The development of multi drug resistance strains of mycobacterium tuberculosis making treatment more expensive and difficult.

HOW IS AID SPREAD? It is caused by HIV which is transmitted through:(i) (ii) (iii) sexual contact (most common way) Infected blood by intravenous drug users sharing needles. From mother to her foetus in the early stages of pregnancy / during birth / through breast feeding.

HOW HIV CAUSES AIDS HIV attaches on CD4 receptors on the T-helper cells and infects them. HIV is a retrovirus, and takes over the host DNA and replicates. By the time the new viruses leave the host cell (T-cell), it is already damaged. Meanwhile, the host T-killer cells recognize and destroy some of the heavily infected T-helper.

Thus, the number of T-helper reduces, and hence activation of many macrophages and T-killer cells does not take place. This undermines ability o the immune system in dealing with other pathogens. Hence, individuals become vulnerable to secondary infection which kills.

CAUSES OF HIV/AIDS INFECTION The rate of infection depends on:(i) (ii) (iii) Nourishment Genetic make up as some are resistant. Medical treatment if provided, can increase life expectancy.

However, there are four main stages:(a) Acute HIV syndrome: Within the first few weeks of infection, the symptoms include fever, headaches, tiredness and swollen glands. 3 12 weeks after infection HIV antibodies appear in the blood making them HIV positive.

(b) Asymptomatic or chronic stage All the symptoms disappear. This may last several years for well fed and taking anti-acids drugs people but a short time for less well fed and without medication. The virus replicates infecting CD4 T-helper cells but is kept in check by the Tkiller cells. Infection to other people unknowingly is very high. Secondary infection may develop as the immune system is depressed.

(c) Sympotomatic disease: Viral load is great and the immune system starts tofail. The T-helper cell count falls from 500 to 200 per mm3 of blood. Patients suffer HIV-related symptoms e.g weight loss, fatigue, diarrhoea, night sweat and infections e.g thrush.

(d) Advanced AIDs As T-helper cell number falls, severe symptoms begin e.g major weight loss, dementia as brain cells are infected, cancer, T.B, menengitis etc. Finally this leads to death.

CONTROL METHODS OF AIDS (i) (ii) (iii) (iv) Education programmes where people will understand how AIDs is spread. Less promiscuous sex Use of condoms Use of clean needles for injecting drugs.

NB: It is hard to get a vaccine as the virus keep mutating, thus the antigens keep changing and the immune system cannot recognize the virus. The mutated viruses are naturally selected hence they replicate fast. Combined drug therapies that are anti-viral stimulate the immune system. These drugs are expensive especially in developed countries. However, they prolong life but do not cure.

HOW INDIVIDUALS MAY DEVELOP IMMUNITY There are various types of immunity:(a) Natural: (i) Natural active immunity: This refers to when the body comes into contact with foreign antigens and the immune system is activated with formation of antibodies and the pathogens are destroyed. (ii) Natural passive immunity: During pregnancy, antibodies from the mother are passed on to the foetus through placenta and also from milk especially colostrums, the baby therefore acquires temporary immune until its own system becomes active. It is short-lived because the antibodies are not replaced. (b) Artificial (i) Artificial passive immunity This takes place when antibodies are formed in one individual extracted and injected into another individual. This is normally done if one is exposed to rapidly acting antigen e.g tetanus (lock jaw) the muscle fibres completely contract due to a series of rapid stimuli and remains in that state. It is due to a toxin produced by the bacterium clostridium tetani. Swallowing and breathing becomes impossible causing death. Anybody exposed to tetanus e.g rusting metal cuts, then they are injected with antibodies against tetanus, preventing development of the disease / death.

(ii) Artificial active immunity In this case, small amounts of antigens (vaccine) are used to produce immunity. The pathogen is made no-infective without reducing its ability to act as an antigen e.g (i) if it is the toxin that causes symptoms, it is detoxified first. (ii) Inactivated viruses or dead bacteria are used as vaccines. (iii) Use of attenuated organisms i.e living but modified so they can produce the disease. (iv) Fragments of the outer-coats of viruses and bacterial, or DNA segments are used as vaccines. The immune system will produce antibodies against antigen and relevant memory cells will be formed. Thus should one come into contact with active antigen it will be destroyed without experiencing symptoms of the disease.

NB: Vaccine based on whole viruses e.g oral polio, stimulates the immune system, but as they become purer, they do not work effectively unless they contain an adjuvant i.e something added to the vaccines to enhance the effects e.g detergents, oil, water, dead bacteria, aluminium hydroxide etc but has nothing to do with specific immune system. They cause inflammation and the worse the inflammation, the more effective the immune system. They alert the body to the presence of a foreign invader by mimicking a characteristic of the pathogens.

IMMUNIZATION AND IMPORTANCE This is the process of protecting people from infection by giving them passive or active artificial immunity. It protects individuals against diseases which might kill or cause harm. It eradicates / eliminates diseases which cause large number of deaths, disabilities or illnesses within a population.

ADVANTAGES OF VACCINATION The child is protected against diseases which could kill or disable. The society benefits as the potential pool of infection is reduced (this protects kids who cannot be vaccinated due to allergies or immune system disease and is known as herd immunity. Most vaccines are relatively cheap compared to cost of treating diseases.

DISADVANTAGES

Some attenuated vaccines are cultured in eggs, to which many children can suffer a violent allergic reaction. Hence, such kids are usually not vaccinated. Few kids become extreme ill after vaccination due to an extreme immune response; some may even die while others have been left severely damaged in the brain. Some scientists suggest that mass vaccination programmes are linked to the recent rise in child hood asthma and allergies.

ANTIBIOTICS AND THE PRINCIPLE BY WHICH THEY WORK These are chemical substances produced by M/o to kill other M/o, and they work by principle of selective toxicity i.e they interfere with the metabolism or functions of the pathogens with minimal damage to human host. HOW DO ANTIBIOTICS WORK? (a) As antimetabolites they interrupt metabolic pathways in M/o causing death e.g blocking nucleic acid synthesis such as sulphonamides. (b) The cell wall agents prevents formation of cross-linking in cell walls, hence bacteria are killed by lusis (bursting) such as Beta lactams e.g pencillin. (c) The cell membrane agents damage the cell membrane thus metabolites leak out or water moves in killing the bacteria e.g some pencillins. (d) Protein synthesis inhibitors they interrupt or prevent transcription or translation of microbial genes thus protein production is affected e.g tetracyclines. (e) DNA gyrase inhibitors they stop bacteria DNA coiling and so it no longer fits within the bacterium e.g quinolone. BACTERIOSTATICS AND BACTERIOCIDALS Bacteriostatics are antibiotics which inhibit growth of M/o. Their effect together with the action of our immune system ensures that pathogens are completely destroyed. Bacteriocidal are antibiotics which kill / destroy almost all pathogens present. This type of treatment is useful when:(i) Treating severe and dangerous infections. (ii) Treating infections where immune system is suppressed e.g transplant patients where the suppressant drugs protect the transplanted organ. (iii) In certain diseases e.g TB/HIV/AIDS

BROAD AND NARROW SPECTRUM Broad spectrum antibiotics destroy a wide range of harmful bacteria, pathogens, neutral as well as good bacteria while a narrow spectrum antibiotics targets one or two specific pathogens.

EFFECT OF DIFFERENT ANTIBIOTICS ON BACTERIA

Agar plate is prepared using aseptic technique. Agar plate is then seeded with a known bacterial culture. Filter paper discs containing different antibiotics or different concentrations of the same antibiotics are placed on the agar and the plate sealed and incubated. A control culture of M/o with known sensitivity to the antibiotic is grown at the same time and under the same conditions. The level of inhibition of bacteria growth gives a measure of the effectiveness of the drug. NB: The wider the clear zone, the effective is the antibiotic.

FACTORS AFFECTING EFFECTIVENES OF ANTIMICROBIAL DRUGS (a) Concentration of the drug in the area of the body infected this determines how easily the drug can reach the tissues. (b) Local PH as this can denature the antibiotics reducing their effectiveness. (c) Susceptibility of pathogen to a particular antibiotics i.e what a doctor would normally prescribe if it successfully destroy pathogens and cures the disease then the pathogen is sensitive to the antibiotic. - If an increased dose of the antibiotic results in successful treatment, then the pathogen is moderately sensitive. - Cases where a particular M/o is not affected by an antibiotic, sometimes even one which may have been effective in the past, then the M/o is said to be resistant. HOW HIV AND MYCOBACTERIUM TUBERCULOSIS SUPPORT THEORY OF EVOLUTIONARY RACE New drugs are being developed, but at the same time bacteria (M/o) keep evolving resistance to these drugs. Thus, there is a constant evolutionary race between pathogens and human beings. An antibiotic is effective only if the M/o has a binding site for the drug or if it interferes with metabolic processes. Mutation help M/o resist effects of antibiotics e.g (i) By making the cell wall impermeable to drugs and such mutations will be selected for when the antibiotic is used; thus bacteria / population becomes increasingly resistant. (ii) By resulting in new biochemical pathways or switch on or acquire a gene for the production of an antibiotic destroying enzymes Again such mutations will be selected for when the antibiotic is used, thus M/o will be ahead in the evolutionary race. This evolutionary race is supported by evasion mechanism shown by:(i) Mycobacterium tuberculosis by producing a thick waxy outer layer which protects them from enzymes of the macrophages. In this state they can remain deep in tubercules, dormant until the person is malnourished /or immune system is weakened.

(ii)

It is sensitive to temperature and stops reproducing at 420c which is way above 400c at which temperature human enzymes begin to denature. The HIV mutates rapidly, that the antigen on the viral coat keep changing after infection making it harder for the immune system to recognize the virus. Selection pressure on the virus is reduced as T-cells count starts to fall. Thus, natural selection favours mutation that enables the virus to replicate fast, allowing it to infect many cells.

NB: Widespread use of different antibiotics to tackle increasing resistance increases the selection for bacteria that are resistant all of them. - This evolutionary race is creating super bugs which are capable of causing death. REDUCING EVOLUTIONARY RACE This can be done by reducing selection pressure for resistance by using antibiotics sparingly, only when strictly necessary, at the same time using few different antibiotics as possible. HOSPITAL ACQUIRED INFECTIONS / HEALTH CARE ACQUIRED INFECTIONS These are infections which are commonly acquired in hospitals and care homes, where people are already frail, ill and where surgery and antibiotics use are high e.g methicillin resistant staphylococcus aureus (MRSA) and clostridium difficile patients who become infected have to:(i) (ii) (iii) (iv) Stay in hospital much longer The cost is high It causes suffering to people Some people even die

EFFECTS OF MRSA Staphylococcus aureus is found on skin of some people or in their nasal passages (non-pathogenic) In the body it can cause boils or infections throughout the body e.g septicaemia Mutations have occurred in some bacteria thus producing penicillinase which breaks down methicillin making them useless (hence MRSA). Thus winning the evolutionary race.

EFFECTS OF CLOSTRIDIUM DEFFICILE It is anaerobic bacterium found in large intestines of a small population 5%.

It is not affected by most antibiotics and produces spores which ensure its survival several months outside human body. In a healthy person it causes no problems as its numbers are limited by competition with gut flora. It produces two different toxins that damage the lining of the intestines causing severe diarrhoea, resulting to bleeding from the gut and even death. A new strain of C. difficile had its gene that limits toxin level mutated thus producing even higher levels of toxin than normal. This therefore causes more serious diseases and more death.

Code of practice relating to antibiotics prescription due to hospital acquired infections: That antibiotic should be used only when it is necessary. Every course of antibiotics should be completed (as the immune system is unable to cope with large number of bacteria, and are not destroyed thus some will become resistance and escape to infect other people. Use of different antibiotics encourages a faster evolution of multiple resistances hence there is need to be understood by general public that they should stop demanding for antibiotics for minor infections as well as stop taking medicine as soon as they feel better.

Codes of practice in relation to infection, prevention and control due to hospital acquired infections.

(a) Hygiene measures: Good hygiene in hospitals and care homes e.g washing of hands by doctors, nurses etc using alcohol based gel between patients to destroy pathogens. NB: Spores of clostridium difficile are not destroyed by alcohol gels and require chlorine based disinfectants. Guidelines about clothing for doctors and other staff e.g long ties which might dangle and carry bacteria from one patient to another are now banned including wrist watches, long-sleeved shirts etc. Thorough cleaning of hospital wards, toilets, bed sheets etc especially for disease caused by c. difficile.

(b) Isolation of patients: Those affected by health-acquired infections need to be isolated from other patients into separate rooms to minimize disease spread. (c) Prevention of infection coming into the hospital:

By screening patients as come thus people with MRSA can be treated immediately and isolated till bacteria have been destroyed. - People visiting patients may bring infections into the wads e.g MRSA - Hence, hospital management advice people not to visit if unwell but ignore the advice. (d) Monitoring levels of health-care acquired infections: It is mandatory for hospitals to measure and report on levels of MRSA and C. difficile infections to government and public in general for measures to be taken. DETERMINING TIME OF DEATH OF A MAMMAL (a) Body temperature: The normal body temperature is 370c. At death, the metabolic reactions which have created the body heat begin to slow and eventually stops. The body loses heat by radiation, convection and conduction. Thus, temperature plateaus for a while before dropping steadily to room temperature. Thus, temperature of the body can give an indication of how long a person has been dead.

(b) Rigor mortis: Muscle cells have large stores of ATP and glycogen, thus can respire anaerobically after death. ATP is needed to maintain the muscles in a relaxed state. But as ATP get finished, muscle fibre become permanently contracted forming a stiffening effect known as rigor mortis. - This process starts about 2 4 hrs after death but takes 6 8 hrs to take full effect. - It starts from the muscles of the face, neck etc and progresses down the body.

NB: Rigor mortis depends on:(i) level of ATP in muscles at the time of death. (ii) Level of activity before death e.g it sets in faste in drowning victims as they use a lot of ATP in struggling to float. Rigor mortis takes about 36 38 hrs after which the muscles soften as enzymes from lysosomes begin to breakdown the tissues. (c) Stages of succession: A dead body is a fleshly available habitat where succession takes place which allows forensic specialists to date time of death accurately.

The first colonizers (pioneers) are anaerobic bacteria that are confined to the gut and as enzymes break down cells, the bacteria spread. Flies like blow flies are then attracted to moisture and smell around the natural orificies as well as open wounds. They lay eggs, maggots hatch and begin to feed on the tissues breaking them down. They pupate, then flies, mate and the cycle starts all over again. Beetles start to lay eggs which hatch into larvae which feed on maggots. Parastic wasps lay their eggs in the fly and beetle larvae. Cheese and coffin flies then move in and by now the body is too dry for maggots. Beetles species with strong chewing mouth parts move in e.g carcass, ham and hide beetles which feed on remains of muscles and connective tissue. Finally, mites and moth larvae feed hair till dry bones are left.

NB: Decomposition rate depends on:(a) Temperature (b) Level of exposure e.g a buried body decay slowly than body left in the open air.

(d) Forensic entomology (study of insects life as it relates to crime): Forensic entomologists know the detailed life cycles of blow flies + other insects that colonize dead boddies and how they are affected by environmental conditions e.g temperature. Using this evidence one can estimate how long a body has been dead e.g if a body is found and no evidence of blow fly activity then it must have been there for no more than 24 hrs. Blow flies layeggs in natural openings of the body e.g eyes, nose, mouth as well as knife and gunshot wounds. Eggs hatch into larvae, then changes to pupa which turns into adults. The time taken from one stage to next differs e.g blow flies 23hrs Egg Larva 27hrs Larva 22hrs Larva 130hrs Pupa 143hrs Adult

On discovering the body, eggs/maggots/ and pupae are collected, and grown to adult so that precise identification of the species of fly / beetle can be made and hence calculating of time of death.

NB: Use of pigs is a better way as it would be difficult to get permission to bury human bodies just for observation.