Unit 4-Biology

Photosynthesis.

 Basically organisms are classified into two groups according to their source of energy:
 Autotrophs – make their own food organic compounds from CO2 e.g. plants
 Heterotrophs- feed on already made food e.g. animals.
 The ultimate source of energy in the universe is the sun.

ATP (adenosine triphosphate)

(See pg. 10 for structure)

It consists of:

 Adenine (organic base)

 Ribose sugar (pentose)
 Phosphate group

It’s the source of energy in all cells

ATP is formed when ADP (adenosine diphosphate) combines with phosphate using energy from respiration, a process
called phosphorylation

ADP + phosphate ATP (phosphorylation)

 The process requires enzyme ATPase and about 34 KJ of energy.

 For energy to be produced the third phosphate is released in a process called hydrolysis

ATP ADP + phosphate (hydrolysis) + about 34kj of energy

(See pg. 11)

ATP can also be formed when electrons are taken by carriers from high energy levels, energy is given out that combines
ADP and phosphate to form ATP.

Photosynthesis mostly takes place in the leaves.

(Sketch and label the external and internal structure of the leaf)

The following parts of a leaf are important.

Epidermis

 Gives rise to waxy cuticle that prevents excessive loss of water (transpiration)
 Protects the leaf from mechanical damages.
 Prevent entry of micro-organisms (pathogens)

Palisade mesophyll.

 It’s the site for photosynthesis.

 It contains numerous chloroplasts.

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Spongy mesophyll.

 Contains numerous air spaces

 Enables gas exchange by diffusion.
 Contains some chloroplast so can also carry out photosynthesis.
 Use as storage for oxygen from photosynthesis which can be used for respiration.

Xylem.

 Transports water and dissolved mineral salts from the soil to the leaves.

Phloem.

 Translocate manufactured food like sucrose, amino acids from the leaves to other parts of the plant.

Guard cells.

 Controls opening and closing of the stomata.

 Contains some chloroplast hence can carry out photosynthesis

Adaptations of the leaf to photosynthesis.

 Broad hence provides large SA for absorption of light.

 Palisade located on the upper surface hence can obtain maximum light for photosynthesis.
 Network of veins with xylem to supply water for photosynthesis.
 Large number of stomata on the lower surface for gaseous exchange.
 Thin to reduce diffusion distance.
 Transparent cuticle to allow light to pass through.

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(Draw the structure of palisade cell and chloroplast pg. 12)

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How the structure of chloroplast is related to its function.

 They have variety of pigments which traps a variety of light wavelengths.

 Have many membranes i.e. grana and thylakoid which provide a large SA for attachment of pigments.
 Thin membrane to allow passage of light.
 Stroma has enzymes required for the process of photosynthesis.
 A lot of ATP synthase molecule in the thylakoid membrane to produce ATP in light-dependent stage.

Within the granum, there exist different types of pigments that absorb light i.e.

 Chlorophyll a
 Chlorophyll b
 Carotene (orange)
 Xanthophyll (yellow)
 Phaeophytin etc.

Each of the pigment has a particular wavelength of light it absorbs.

The photosynthetic pigments can be divided into two main groups:

Primary pigments.

 They are two types both of which are specialized forms of chlorophyll a and one is designated as P680 and the
other P700.

Accessory pigments.

 Include all other forms of chlorophyll and carotenoids. They pass on their energy to the primary pigments which
emit electrons which causes the light dependents reaction to take place.

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(See an experiment on how to get different pigments from a leaf pg. 13)

Photosystems.

 This refers to how photosynthetic pigments are organized. They are chlorophyll complexes.
 Are of two types:
 Photosystem I (PSI)- contains primary pigment P700 and accessory pigments. They absorb light at wavelength
700nm
 Photosystem II (PSII)- contains primary pigment P680 and accessory pigments. They absorb light at wavelength
680nm

THE PROCESS OF PHOTOSYNTHESIS.

Occurs in two stages:

 Light-dependent stage
 Light- independent stage.

Light – dependent stage.

 Takes place in the thylakoid/lamella/granum in the presence of light.

 Light strikes the leaves, electrons from PSI and PSII are excited to a higher energy level.
 They are released and taken up by electron acceptors.
 The electrons from PSII are taken up by electron carrier to PSI.
 In the process ADP is phosphorylated to ATP.
 Water in the chloroplast undergoes photolysis and forms:
 Oxygen gas which diffuse out through the stomata.
 Electrons from water replaces those lost by PSII
 Protons are also obtained from water and they combine with electrons rom PSI forming hydrogen atoms which
reduces NADP to reduced NADP
 Some of the electrons from PSI may go back via electron carriers to PSI and ATP molecules are formed from
ADP.
 This process is called cyclic-photophosphorylation
 When ATP is formed by electrons without going back to where they came from, then its termed as non-cyclic
photophosphorylation

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Difference between cyclic and non-cyclic photophosphorylation.

Non-cyclic photophosphorylation Cyclic photophosphorylation

Uses PSI and PSII Uses PSI only

Involves photolysis of water No photolysis of water

Water is the electron donor Chlorophyll a (P700) in PSI

Final electron acceptor is NADP Final electron acceptor is chlorophyll a (P700) in PSI

Products are Reduce NADP, ATP and oxygen Product is ATP only.

Light independent stage.

 Takes place in the stroma.

 Carbon dioxide from the atmosphere 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.
 The CO2 combines with a 5-carbon compound called ribulose bisphosphate (RuBP) with the help of an enzyme
called RUBISCO (ribulose bisphosphate carboxylase) to form an unstable 6-carbon compound intermediate.
 The 6-carbon intermediate breaks down into 2 molecules of 3-carbon glycerate-3-phoaphate (GP)
 The 2-GP are then reduced using hydrogen from reduced NADP to form 2 glyceraldehyde 3-phosphate (GALP).
This uses ATP from light-independent stage.
 NADP is regenerated and returned back to light independent stage.

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  Pairs of GALP combine to form intermediate hexose sugar which undergoes condensation to form
polysacchande e.g. starch.
 Some of the GALP are converted to RuBP with the help of ATP for the process to continue.

TP = GALP

The glucose formed can be used to form other compounds e.g.

 Used as fuel for respiration

 Combine with nitrates from soil to form amino-acids which form proteins.
 Combine with phosphates and form building block for nucleic acids.
 The GP can be converted to pyruvate from where fatty acids are formed which combine with glycerol to form
lipids

Factors affecting the rate of photosynthesis.

 Light intensity
 Temperature.
 CO2 concentration.

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A limiting factor is that which when increased increases the rate of reaction and vice versa.

0.13% CO2, 300C

C 0.13% CO2, 200C

B 0.03% CO2, 300C

D A 0.03% CO2, 300C

Light intensity

Explain the limiting factor for graphs

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ECOLOGY

Key terminologies.

 Habitat- The place where an organism lives. E.g mountain, forest, pond etc
 Microhabitat- Smaller area within the habitat where an organism lives e.g tree within a forest
 Population- A group of organisms of the same species living and breeding together in a babitat.
 Community- A group of organisms of different species in a habitat.
 Niche- The description of the habitat of an organism and the role of that organism in that habitat.
 Abiotic factors- These are the none-living elements of an ecosystem. E.g. light, temperature, rainfall etc.
 Edaphic factors- Are soil factors e.g. soil pH, structure, texture etc.
 Biotic factors- These are living elements of an ecosystem. E.g. predators, preys parasites etc.
 Biosphere- Part of the earth that is habitable by living things.

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  Ecosystem- All the organisms living in a particular area and their interaction among themselves and with the
environment.
 Abundance- The number of organisms of one species in a particular area(= population size)
 Distribution- Where species occupy within a particular area.
 Producers- Organisms that make their own food by the process of photosynthesis (plants)
 Consumers- Organisms that depend on others for food (they do not make their own food). May be primary,
secondary, tertiary or quaternary consumers.
 Trophic level- Feeding level in an ecosystem. E.g. 1st trophic level = producers, 2nd TL = primary consumers………

ENERGY TRANSFER IN AN ECOSYSTEM.

The sun is the ultimate source of energy in an ecosystem.

This energy enters the ecosystem through plants during photosynthesis.

When sun (solar) energy from the strikes the leaf, not all is used for photosynthesis but:

 Some is lost by evaporating water on the surfaces of the leaves

 Some reflected by the leaf surface
 Some penetrate the leaf surface but not used for respiration.

Solar Radiation

To evaporate water reflected off the leaf

Transmitted but not used

Used for photosynthesis

 The solar energy used in photosynthesis forms the Gross primary productivity (GPP)
 GPP is the total amount of chemical energy captured by green plants in the process of photosynthesis.
 It’s defined as the rate at which energy is incorporated into the biomass of plants
 Biomass is the mass of an organism when all water is removed. It’s the mass of an organism per unit area of
ground or water.
 The unit for biomass is KJm-2yr-1 / Kgm-2yr-1
 The unit for GPP is also KJm-2yr-1
 Net primary productivity (NPP) is the amount of energy from plants that is available for consumption after
respiration has taken place. (It’s the energy stored in the body tissue).
 The unit for NPP is also KJm-2yr-1

GPP = NPP + R

NPP = GPP - R

Complete the table below:

Mature rainfall (S America) Alfalfa field (USA) Young pine forest (UK)

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GPP 188,000 102,000 51,000
R 134,000 20,000
NPP 64,000

i) Calculate the values for respiration by plants in the alfalfa and the NPP of the young pine

ii) How much energy is available to the primary consumers in the rain forest?

iii) Suggest why the GPP of the rainforest is much greater than that of the pine forest.

iv) Suggest why the NPP of Alfalfa field is greater than that of the rainforest.

In essence only about 10% of energy is transferred from one trophic level to the next.

About 90% is lost in various ways i.e.

EF
EC

EC EU
EA

EP

ER

EC= energy consumed

EF= energy lost in feaces

EA= energy Assimilated

EU= energy lost in urine

ER= energy lost in respiration

EP=NPP = energy of production (increasing the biomass)

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Only about 10% of energy is transferred to the next level because:

 Some of the energy formed by plants are used for respiration.

 Not all parts are eaten by the next trophic level.
 Not all parts eaten are digested and a lot of energy are lost as undigested food.
 Some energy is lost through respiration.

Using the photocopy to answer the following questions.

1) What is the GPP of grasses and herbs?

2) What is the photosynthetic efficiency? (the efficiency of conversion of incident solar energy to GPP)

3) What is the NPP of

i) Seed eating birds

ii) Common green grasshopper

iii) Spiders

4) How much energy is lost through respiration and feaces by field mice?

5) Which organisms are heterotrophs?

Efficiency of energy transfer.

This is the proportion of energy used to make biomass compared with energy available to an organism in the
trophic level.

𝑒𝑛𝑒𝑟𝑔𝑦 𝑡𝑟𝑎𝑛𝑠𝑓𝑒𝑟𝑒𝑑 𝑡𝑜 𝑜𝑛𝑒 𝑡𝑟𝑜𝑝ℎ𝑖𝑐 𝑙𝑒𝑣𝑒𝑙

Efficiency = x 100
𝑒𝑛𝑒𝑟𝑔𝑦 𝑡𝑟𝑎𝑛𝑠𝑓𝑒𝑟𝑒𝑑 𝑡𝑜 𝑝𝑟𝑒𝑣𝑖𝑜𝑢𝑠 𝑡𝑟𝑜𝑝ℎ𝑖𝑐 𝑙𝑒𝑣𝑒𝑙

EET varies due to:

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  Effort required to find food
 Digestibility of the food
 Metabolic rate of the organism

From the photocopy, calculate EET at:

i) 1st trophic level

ii) 2nd trophic level

iii) 3rd trophic level

Use the above to calculate the EET between secondary consumer and primary consumer.

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 EFFECTS OF ABIOTIC FACTORS ON THE DISTRIBUTION AND ABUNDANCE OF ORGANISMS

Light.

 Light intensity affects rate of photosynthesis and GPP. All organisms depend on photosynthesis hence light
will affect their distribution and abundance. Increase in LI will increase photosynthesis and GPP hence
abundance of organisms will also increase.
 Plants under low LI usually:
 Reproduce early to avoid shade by larger plants
 Have extra chlorophyll/ pigments sensitive to lower LI
 Have increase leaf SA
 Photoperiod also affect germination and flowering in plants and reproductive behavior in animals hence
distribution and abundance.
 Animals are affected by the distribution of food (plants and other animals)
 More light, more photosynthesis, more food and more animals.

Temperature.

 Extreme temperature affects the activity of enzymes in plants and ectothermic animals. This affects
metabolic reactions in the body of plants and animals.
 Organisms have optimal temperature at which they grow and reproduce. Above or below that reproduction
does not take place easily hence abundance and distribution is affected.
 Extreme temperature may also cause migration, hibernation of animals.
 Plants loss excess water if temperatures are too high
 Organisms have evolved Behaviour and physiological features to survive extreme temperatures.

Wind and water current.

 Wind increases water and heat loss from organism’s body. This affects their distribution and abundance.
 Wind destroys forests and community within it.
 Strong water current destroys and kills aquatic organisms especially during flooding. Organisms must be strong
swimmers to survive or have strong attachment features

Water availability.

 Affected by precipitation, rate of evaporation and edaphic factors like drainage.

 Where water is scarce, only organisms well adapted can survive e.g. xerophytes.
 Too much water increases the population of some organisms while may affect others especially flooding.
 In terms of plants we have:
 Hydrophytes- in places with excess water

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  Mesophytes- in places with moderate water
 Xerophytes- in places with scares water.

Oxygen availability.

 Cold or fast moving water contain sufficient oxygen to support life .

 Increase in temperature and stagnation lowers the amount of oxygen in water which affects the survival of
aquatic organisms.
 In waterlogged areas, air spaces are occupied by water and roots are deprived of oxygen and may cause death
of plants. To survive such plants must have special adaptations to enable them survive.

Edaphic factors.

 Soil structure affects the distribution of organisms. Sandy soil hold less water hence can support little plants.
 Leaching is high in sandy soil and this may lead to reduced mineral content of the soil hence population density
of the plants
 Clay soil supports more plants than sandy due to its texture
 Loam soil is a mixture of sandy and clay and supports a wider range of plants.

EFFECTS OF BIOTIC FACTORS ON THE DISTRIBUTION AND ABUNDANCE OF ORGANISMS

Predation.

 Predator is an organism which feeds on all or parts of another organism called the prey.
 As the prey population increases, there will be more food for the predators and after an interval, the predator
population increases.
 As predators increases they will eat more pray than they are replaced by reproduction and thus the number of
the prey will begin to fall.
 This then reduces food supply of predators and thus they will not produce many offsprings, while some die and
the number falls.
 This allows the abundance of the prey to increase again e.g. larynx and the hare.
 If a graph id drawn of time vs. population then a predator-prey relationship graph is obtained which has
oscillations of the prey and the predators which are out of face.

Finding a mate

 Most animals cannot reproduce by themselves and they require mates ( males and females) which in turn
have an effect on the abundance of the animals present.

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  In plants if a seed is dispersed to a new area, it germinates and survives but its unlikely to be permanent,
unless other plants of the same species grow in the same area or the plant is able to reproduce asexually.

Territory.

 Its area held and defended by an animal or a group of animals against others organisms which may be of
the same or different species. E.g. the male tiger which mark their territory by scratching trees and
urinating. This ensures that after breeding the young ones will be able to survive as there will be food and
lack competition

Parasitism and diseases.

 A parasite is an organism which depends on other organisms, referred to as the host, for food and shelter.
 They therefore weaken their hosts and may cause diseases.
 Diseased animals will be weakened and do not produce successfully while sick predators cannot hunt well,
while preys that are sick likely to caught by the predators.
 Some diseases are highly infectious and can spread without direct contact.
 Communities with greater biodiversity normally have fewer effects of the diseases.

Competition.

 This refers to when two or more organisms compete for the same resource which is in limited supply e.g.
abiotic resources like light, mineral etc. and biotic resources like territory, mates etc.
 Competition are of two types:

Intraspecific competition- between members of the same species.

Interspecific competition- between members of different species

 In both the organism which is well adapted usually survives and the other eliminated.

Density dependent and density independent factors

Density dependent factors

 Are factors which increase as the population increases.

 Are mostly biotic factors e.g. competition, predation diseases etc.

Density independent factors.

 Are factors that that affect the population regardless of the population size.
 Are mostly abiotic factors e.g. temperature, light intensity etc.

SUCCESSION.

This is the process by which communities of organisms colonize a given area over time and are replaced by other
different communities.

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Are of two types:

Primary succession.

 Occurs when the starting point is a bare rock or a sand dune normally seen after a volcanic eruption.
 The 1st organisms to grow are called pioneer species (opportunistic species) e.g. lichens, mosses, algae etc.
 They break the rocks into grains (weathering) and trap organic matter that breakdown humus.
 The grains + organic matter form soil.
 Ferns, grasses and small herbaceous plants can establish themselves replacing the pioneer species.
 The action of the roots and the humus they form when they die decay and increase amount of soil.
 The soil layer develops and more water and nutrients are retained and become available for plant roots such as
shrubs which can now grow.
 Plant and animal diversity increases.
 Finally a climax community is formed. This is a community where the biodiversity and the range of species are
generally constant.

Explain the meanings of:

 Climatic climax community

 Plagio/Biotic/deflected climax

Secondary succession.

This is the evolution of an ecosystem from existing soil that have been cleared of vegetation. e.g. after fire, flood, etc.

Plants may start growing in such area if:

 Seeds and fruits are dispersed from other areas.

 Some parts of the plant remained underground and start growing e.g. roots, rhizomes when conditions become
condusive.
 Encroachment from the neighboring plants e.g. runners

The different stages of succession are called seral stages.

 For primary succession:

Algae, moss, lichens ferns grass shrubs/young forest mature forest

 For secondary succession e.g.:

Grass weeds grass stage grass & shrubs young forest, pine, young hardwood mature forest

Difference between primary and secondary succession.

Primary succession Secondary succession

Begin with bare rock Begin with soil
Pioneer species are lichen, algae and mosses Pioneer species vary
Take long time to establish Take short time to establish
Low biodiversity High biodiversity

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  It’s important to note that since the soil in secondary succession is very rich in humus, it has high water holding
capacity and mineral salts hence can support large number of plant and species

CARBON CYCLE.

See pg. 38 for diagram.

 The amount of CO2 in the atmosphere is about 0.035%

 Carbon exist in form of CO2

CO2 is removed from the atmosphere by:

 Photosynthesis
 Dissolving in water bodies

CO2 is returned to the atmosphere by:

 Respiration
 Combustion
 Volcanic activity
 Decomposition/decay

Carbon is passed from producers to animals by feeding

 The remains of dead and decaying organic matter are converted to fossil fuel by fossilization.
 They also undergo sedimentation and converted to carbonate rocks.

CARBON SINKS

 These are reservoirs where carbon removed from the atmosphere is locked up in organic or inorganic
compounds.
 The most common carbon sinks include:
 Bodies of living organisms (biotic system)
 Rocks e.g. limestone, fossil fuel.
 Ocean-dissolved CO2 and by photosynthesis of the phytoplankton, making shells of animals.
 The quantity of carbon stored in carbon sinks is measured in pentagrams.
 1 pentagram = 1 x 1015g or 1 billion tones.
 Carbon cycle is self-regulating. That is the amount of carbon released in respiration and other natural processes
and that which is absorbed in photosynthesis remains in balance.
 Human activities can alter this balance.

Role of micro-organisms (decomposers) in regulating carbon

 The decomposers secrete enzymes from their bodies which diffuse to the dead decaying organic matter and
digest them (extra-cellular digestion)

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  The mineral ions released e.g. nitrates and phosphates dissolve in water and move into the soil where they are
used by the plants.
 The digested food e.g. glucose diffuses back into the decomposer where they undergo respiration giving out
CO2 which is then used by plants for photosynthesis.

GLOBAL WARMING

This is the average increase in the temperature of the earth’s surface over a period of time due to the effect of
greenhouse gasses.

It’s usually caused due to accumulation of greenhouse gases in the atmosphere.

The greenhouse gases include:

CO2

 Forms about 9-26% of the GHG

 Mostly from combustion of fossil fuel, motor vehicles, deforestation, respiration etc.

Methane.

 About 4-9% but has about 72 times greater effect than CO2
 Formed by the action of bacteria on wet, dead decaying organic matter e.g. rice paddy fields which are normally
waterlogged and have bacteria which release methane as they grow.
 Also from digestive system of ruminant e.g. cows. If these animals burp and release methane gas.
 The amount of methane they produce depend on:
 The breed of the cow.
 The type of food eaten (adding concentrates to diet reduces methane emission since they are easier to digest
however production of concentrate produces CO2 which is also a GHG)
 Weather the cow is giving milk. The higher the number of lactations, the less the emission of methane.
 Health and age of the cow.
 Why is the amount of methane increasing?
 Increase in population leads to more rice production hence more methane

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  More milk production hence more methane

(See page 41)

Water vapour.

 About 36-70% and is mostly from plants during respiration, evaporation from water bodies, respiration from
organisms

Ozone (O3)

 About 3-7%. Formed when an oxygen atom combines with oxygen molecule in the presence of UV light.

CFCs

 From refrigerators, spray perfumes etc.

How global warming occurs.

 The sun radiation reaches the earth’s surface in form of short wavelength infra-red radiations.
 Some are absorbed while others are reflected back into the space as long wavelength infra-red radiations.
 The greenhouse gasses absorb the long wavelengths and re-radiate them to the earth’s surface leading to the
warming of the earth’s surface.

(See page 40)

Evidence of global warming.

1. Metrological Departments.

 Temperature records can give a clear indication of changes in earth’s temperature over time.
 Analysis shows that there has been a general rise in the earth’s temperature.
 The other evidences are called temperature proxies and include:

3. Frozen isotopes

 Involves drilling down of ice and analyzing the air that is trapped in different layers.
 Records of oxygen isotopes in melted ice i.e. proportion of O16 and O18 reflects the air temperature at the time
the ice layer was laid down.
 Analysis shows that that there has been increase in temperature over time.

3. Dendrochronology.

 This is the dating of past events using tree ring growth.

 The rings are formed annually by cell division within the rings.
 The thickness of the ring depends on the climate when the rings were formed.
 When its warmer the rings are thicker (because the conditions for growth are better)
 By looking at the changes in thickness of the rings, one can easily conclude on changes in temperature.

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  Over time, it seems the rings are becoming thicker indicating rise in temperature.
 Age of the tree can also be determined by counting the rings.
 For reliability, one needs to compare results of the same species in different places.
 One challenge of dendrochronology is that other factors may also affect the thickness of the rings (growth) e.g.
rainfall, sunshine, CO2 concentration, rainfall etc.

4. Pit bogs.

 They are made of partly decomposed plant materials.

 Peat bogs are acidic, cool and anaerobic hence prevent bacteria from decomposing the organic matter.
 Pollen is often preserved in peat bogs.
 The peat bogs accumulate in layers so age of the preserved pollen increases with depth.
 Pollen grains can be obtained from the cores from the different layers.
 The plant species of the pollen obtained can be identified.
 Since the temperature at which such plants grow, they can be used to estimate the temperature of that time.
 Gradual increase in pollen from a plant species that’s more successful in warmer climate would show a rise in
temperature.

5. Increased levels of CO2

 Readings of CO2 concentration have been taken at intervals on hourly basis in Mauna Loa.
 Records show that the level CO2 in the atmosphere have greatly increased.

Dendrochronology and pit bogs are used to confirm radio-active dating in a process called wiggle matching.

Predicting the future.

 This can be done by extrapolation of data on greenhouse gasses to make a prediction of the future
temperature.
 Graphs can also be drawn from the data to help in the prediction.
 Computer models can also be used to predict the future.

Limitations of extrapolation:

 It’s impossible to tell exactly the impact of CO2 on global warming because there are other factors that involved
e.g. human activity, methane.
 It’s impossible to predict the impact of global warming on particular aspect of world climate. This is because the
effect of global warming can be different for different ecosystem.
 Extrapolation do not take into account unknown factors in the future e.g. technological advancement, etc.

Effects of global warming.

Risk of flooding.

 This due to increased volume of water bodies and rise in sea levels

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Climatic changes.

 Rise in temperatures affect the climate and rainfall patterns

 Change in species distribution.
 Increase in temperature may lead to extinction of some organisms
 Migration etc.

Effects on organisms.

Increase in temperatures may:

 Affect working of enzymes

 Growth in both plants and animals
 Reproduction
 Seasonal cycles
 Availability of food

It’s important to come up with programs that may help reduce global warming.

These may include:

 Afforestation /reforestation programs

 Alternative sources of energy (use less fossil fuel)- use biofuel

Limitations of these programs.

 Lack of agreement within the scientific world on the actual causes of GW.
 Political influences and pressure groups may be bias on their views.
 Alternative views by industrialists to avoid legislation that may affect their industries.

It’s also important to establish if any causal and correlation relationship on any factor.

 Causal relationship is where one factor directly causes an effect e.g. burning of fossil fuel increases CO2 level
 Correlation is where a factor appears to be linked to a change/event e.g. increase in CO2 and global warming.

SPECIATION AND EVOLUTION.

It’s important to recall these key definitions:

 Genome- this refers to all the DNA in an individual.

 Proteome- all the proteins produced from DNA in an individual.

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  Proteomics- study of different proteins and how they come about.
 Mutation- sudden changes in the genetic material of an organism.
 Gene pool- total number of genes in a given population.
 Allele- alternative forms of a gene.
 Allele frequency- relative occurrence/frequency of a particular allele in a population.
 Gene family- groups of closely related genes.
 Evolution- process by which species of living organisms undergo permanent change as a result of natural
selection in response to changes in the environment.

(See the effect of gene family on page 55)

SPECIATION.

This is the process by which new species are formed from a population.

Species is a group of closely related organisms capable of interbreeding to produce fertile offspring.

Speciation can occur by:

Allopatric speciation.

 Occurs when populations are separated by geographical barriers.

 Such species are formed depending on climatic changes

G. Barrier climatic change Natural selection reproduction large population increased allele F

Sympatric speciation.

 Occurs when new species are formed in other ways other than geographical isolation i.e. reproductive isolation.
The organisms live together but still can form other species.

(Describe hoe apple maggots can be described as a new species emerging. Page 56)

The role of reproductive isolation on speciation

Reproductive isolation occurs by:

Prezygotic barriers

Occurs when fertilization is prevented. This may be due to:

 Habitat isolation- when populations select different habitats in the same area and thus do not come into
contact during reproductive seasons.

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  Temporal isolation- occurs when organisms have very brief mating or flowering periods. Unless this is
synchronized, the mating will be impossible.
 Mechanical isolation- due to physical barriers to fertilization. E.g. the position of sex organs may prevent
mating.
 Behavioral isolation- organism may fail to recognize other members of the same species due to changes in
behavior.
 Gametic isolation- one gamete may fail to attract the other gamete or male gamete may fail to penetrate the
female gamete.

Postzygotic barriers.

In this case, fertilization takes place and zygote may not grow to maturity and if they do, thy may not reproduce. This
may be due to:

 Low hybrid zygote vigour

Here, the zygote fails to develop properly and dies during embryonic development or if formed they will have
abnormalities and cannot reproduce successfully.

 Low hybrid adult viability.

The offsprings are formed but fail to thrive and grow properly.

 Hybrid infertility.

The offspring formed are infertile and cannot reproduce.

New evidences of evolution.

 From DNA profiling. (DNA evidence)- This is the observation made at the non-coding areas of DNA to identify
patterns which are unique to individuals and are used to identify relationship between individuals and species.
 Organisms that developed from others seem to have a more similar DNA.
 Proteomics. - Related organisms have similar DNA sequence and so similar amino acid sequence in the protein.
 Those organisms that diverged away from each other more recently should have more similar proteins as less
time has passed for changes to occur.

(See page 58-61)

How scientists validate the evidences of evolution.

This is done by sharing and discussing their finding to make sure its valid and reliable through:

Scientific journals.

 This is an academic magazine where scientists publish articles describing their work.
 Here they share ideas, theories, experiments, evidences and conclusions.
 Through this they can repeat the same experiment to see if the results can be replicated.

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  If the results are replicated over and over, then the results can be said to be reliable.

Peer review.

 Here other scientists in the same field read and review the work.
 The peer reviewer must check if the work is valid and supports the conclusion.

Scientific conferences.

 Here they discuss each other’s work, ask questions and get clarifications.

INFECTION, IMMUNITY AND FORENSICS

Determination of time of death.

Forensic science have been use to determine the time of death (TOD) especially in murder cases.

This can be done by:

1. Body temperature.

 All mammals produce heat from metabolic reactions e.g. reparation. For man these maintain the body
temperature at about 370C
 After death these metabolic reactions begin to slow down and eventually stop causing the body temperature to
all until it equals the surrounding temperature. This is called algor mortis.
 The body also losses heat by radiation, convection and conduction.
 The body cools at the rate of about 1.5 – 2.00C per hour hence scientists can easily calculate the time of death.
 However the rate at which the body cools depend on:
 Body size
 Temperature of the surrounding (ambient temperature)
 Clothing
 Body hair

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2. Rigor mortis.

 This is the stiffening of the body muscles.

 This occurs when the body is deprived of all ATP since ATP is needed for relaxation of the muscles.
 Also when body is deprived of oxygen, the cells respire anaerobically leading to build-up of lactic acid
 This lowers the pH of the cell inhibiting the enzymes that produce ATP.
 RM starts from smaller muscles in the face, neck and progresses down the body.
 It starts about 2-4 hours after death but takes 6-8 hours to take full effect.
 It takes about 36-38 hours after which the muscles soften as enzymes from the lysosomes begin to break down
the tissues.
 The rate at which RM sets in depends on:
 Level of ATP in muscles at the time of death
 Level of activity before death. (those who struggle during death use more ATP hence RM sets in faster
e.g. one who drowns)

3. Forensic entomology.

 This is the study of insects’ life as relates to crime.

 Forensic entomologists know the detailed life cycle of insects e.g. blow flies
 Changing from one stage to another takes specific time and this can be used to determine time of death.
 For example blow fly leave hatch from eggs about 24 hours after they are laid. If only blow fly eggs are found on
a body, you could estimate that the TOD was no more than 24 hours ago.

(See page 70)

4. Stages of succession.

 The type of organisms found in a dead body changes over time going through a number of stages. This is called
succession.
 TOD can be established from the particular stage of succession that the body is in.

(Outline stages of succession on page 68)

Successions in animals almost resemble that of plant but differ in the following ways:

Plants Animals

Pioneer spies are algae, lichens Pioneer species are anaerobic bacteria

Takes a longer time Takes a shorter time

Involves plants and animals Involves animals only

Has climax community No climax community

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5. Extent of decomposition.

 Immediately after death bacteria and enzymes begin to decompose.

 Forensic scientists can use the extent of decomposition to establish a TOD.

Approximate time since TOD Extent of decomposition

Hours to a few days Cells and tissues are being broken down by the body’s own
enzyme and bacteria that were present before death .The
skin on the body begins to turn a greenish colour.

A few days to a few weeks Microorganisms decompose tissues and organs .This produces
gases (e.g. methane), which cause the body to become
bloated .The skin begins to blister and fall of.

A few weeks The tissues begin to liquefy and seep out into the area around
the body.

A few months to a few years Only a skeleton remains.

Decades to centuries The skeleton begins to disintegrate until there is nothing left
of the body.

GENETIC CODE

This is the relationship between the DNA nucleotide bases and amino acids.

Features of genetic code.

 It’s a triplet code- three basses code for a specific amino acid.
 Its universal- all the coons are similar in all organisms.
 Its degenerate- some amino acids have more than one triplet. This is important as it guard against unnecessary
mutations.

Its non-overlapping- each codon is read separately

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  Some codons do not code for any amino acid and are called stop or non-sense codons.

PROTEIN SYNTHESIS

Involve two stages:

 Transcription.
 Translation.

Transcription.

 Takes place in the nucleus.

 It involves formation of complimentary mRNA from DNA.
 The DNA unwinds by breaking the hydrogen bonds using DNA helicase enzyme.
 The basses on the DNA are exposed and they attract complementary RNA nucleotides.
 RNA polymerase joins the nucleotides to form a mRNA strand.
 Phosphodiester bonds are formed between the mononucleotides by the process of condensation.
 The DNA zips up with the help of DNA polymerase.
 mRNA leaves the nucleus through the pores into the cytoplasm.
 The mRNA formed is called pre-mRNA. It contains non-coding regions called introns and coding regions called
exons.
 The introns are removed by the action of enzyme spliceosome in a process called RNA splicing during post-
transcriptional changes.

Translation.

 Takes place in the cytoplasm in the ribosomes.

 Ribosomes attach on the mRNA with the small sub-unit on the lower scale and the large sub-unit on the upper
scale.
 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
terminals 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 tRNA onto the mRNA.

 The same process is repeated by the 2nd tRNA which carries the second amino acids.
 The first peptide bond is formed between the first and the second amino acid by condensation reaction to form
a dipeptide.
 The hydrogen bond between the codon and the anticodon of the first and the 1st tRNA are broken, releasing the
tRNA back to the cytoplasm leaving the amino acid behind.
 In the cytoplasm, the released tRNA combines with specific amino acids with the help of amino acyl tRNA
synthetase
 The ribosome moves enclosing the 3rd codon and the sane procedure is followed until reach the stop/ non-
sense codon i.e.UAA UGA, AUG etc. where protein synthesis stop.

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  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 carbohydrates can be added to form glycoproteins.

How one gene can give rise to more than one protein through post-transcriptional changes to mRNA.

 The RNA transcribed from DNA is called pre-mRNA.

 It contains non-coding areas called introns and coding areas referred to as exons.
 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-slicing when enzyme complex called spliceosome are involved
 Sometimes are removed as well thus the code on the final mRNA is different from the code on the DNA.
 Hence, polypeptides are with slight difference in amino acids formed which in turn produce different proteins.
 Thus, post-transcriptional changes lad to a variety in the phenotype that is coded for directly in the genotype
e.g. human DNA consists of 25,000 genes but coded for more than 90,000 different proteins.

DNA amplification using polymerase chain reaction (PCR)

 PCR adapts the natural process in which DNA is replicated in cell, thus making enough DNA for profiling from
tiny traces. The following are required:-
1. DNA sample to be amplified
2. DNA polymerase
3. Primers i.e. small sequences of DNA which join to separate DNA stands.
4. Good supply of the four nucleotides bases i.e. G, C, A and T.
 All these are mixed together in the PCR machine.
 The mixture is heated to 930c in order to separate the strands by breaking the hydrogen bonds.
 The mixture is then cooled at 550c so that primers join anneal/bind to single stranded DNA by hydrogen bonds
to complimentary portions of 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 DNA.
 The cycle is repeated each time ; the DNA copy becoming the template.

DNA profiling and its use for identification &determining genetic relationship between organisms

 The DNA molecule is separated from the sample.

 it is broken down into fragments using restrictions 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.

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  The dye fluoresce when placed under the U.V light (responsible or DNA bands).
 A 2 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 of the end .
 An electric current is passed through the apparatus and the DNA –fragments move towards the positive
anode.(due to the –ve charge on the phosphate group in the DNA).
 Fragments move at different rate 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: An 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 blot on the filter.
 Radioactive single stranded DNA probes(gene probes) are used to bind to specific portions of the fragment
known as the core

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