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Higher
The Scientific Method
Biology is a science.
Science means ‘to know’.
Biologists want to know the ‘secrets’ of life.
The scientific method is an ordered sequence of investigative steps used by most scientists to explain the phenomena observed in nature.
The steps involved try to remove any bias from the discovery process.
Science can only investigate phenomena that can be observed, measured and tested.
The Scientific Method
Observation Made: must be accurate and unbiased.
Hypothesis Put Forward: a testable possible explanation.
Prediction Made: based on the hypothesis.
Hypothesis Tested: by further observation, experiment or modelling.
Conclusion Drawn on the Results: hypothesis supported or not supported.
Further Testing of the Supported Hypothesis: further checking of its validity.
Theory Established: a hypothesis that has withstood all testing.
Principle Accepted: a theory that has held up against long vigorous testing.
If a hypothesis is not supported then form available knowledge and creative thinking a new hypothesis must be made and tested. And so it continues until a hypothesis, subjected to rigorous testing, is found ‘not false’.
Supported hypothesis are often modified as more knowledge becomes available from its more vigorous testing or new information becomes available from other areas of study.
Experimentation
Hypotheses, laws and principles are often tested by the experimental method.
An experiment is a practical test carried out under very carefully manipulated conditions. Controlled Experiments – a double test
The Control: the procedure without the factor under investigation.
The Experiment: the procedure that includes the factor under investigation.
The control and the experimental procedures must be identical in all other aspects.
Results of control and experiment are compared.
Identical control and experiment results: factor is of no relevance.
Different results: factor under investigation has a significant role.
Repeat the controlled experiment many times to verify the results.
Important Aspects of Good Experimental Procedure
Well planned and designed: the hypothesis will be tested properly.
Safe working: a full and accurate risk assessment each step is vital.
A suitable control must be designed.
Repetition: to verify the results.
Independent Verification: other unconnected scientists must repeat the work exactly and obtain the same results.
No Bias: the appeal of the hypothesis must not influence the procedures or interpretation of the results.
Avoiding Bias
Large sample size: better chance of gaining the true representative average.
Random selection: more likely to produce a ‘regular type’.
Double-blind testing: the investigating scientist and the test subjects do not know the composition of the control or experimental group.
Limitations of the Effectiveness of the Scientific Method
Insufficient Knowledge: Hypotheses about the cause of many diseases were false until vitamins and micro-organisms were discovered.
Method of Investigation: Many secrets of nature remained hidden due to poor instrumentation. Cells, and so the basis structure of living organisms, were not discovered until the development of the microscope.
Inability to Interpret Results: The bursting of animal cells in pure water could not be explained until the kinetic theory of matter was advanced to explain results in a change in the characteristics of a species. Many populations of bacteria are now resistant to antibiotics.
Accidental Discoveries: Mistakes can be learning opportunities. Alexander Fleming discovered antibiotics when a penicillin fungus contaminated a culture of diffusion and osmosis.
Change is an Important Aspect of the Natural World: Evolution by natural selection causes populations to adapt to their environment. Environmental change bacteria on an agar plate.
Nutrition – The Chemistry of Food
Food is material that is a good source of one or more of the following: protein, carbohydrate or lipid.
Living organisms need food for energy, growth, repair, defence and reproduction.
Food often contains vitamins and minerals.
Metabolism
Metabolism is the full set of chemical processes carried out by a living organism (anabolism + catabolism).
Anabolism: the formation of large complex organic molecules by linking smaller simpler organic molecules. Catabolism: the breakdown of large complex molecules into smaller simpler biomolecules.
Anabolic reactions require energy input and catabolic reactions release energy.
Protein
Elements: C, H, O and N in all proteins. Some proteins also contain P and/or S.
Subunits: Amino acids are the subunits that are linked by peptide bonds in chains, folds and branches.
Twenty different amino acids — each different sequence of amino acids produces a different protein.
Each protein has a specific functional shape.
Proteins synthesis takes place at the ribosomes.
Meat, fish, eggs, milk, beans, peas and nuts are good sources of dietary protein.
Structural Role of Protein
Keratin: in hair and outer layer of the skin.
Myosin: major protein in skeletal and cardiac muscle.
Metabolic Role of Protein
Many proteins function as enzymes (specific biological catalysts).
Some proteins function as hormones.
Carbohydrate
Elements: CHO. General Formula: (CH2O)n or CX(H2O)Y
Monosaccharides: single sugar unit
Pentoses: C5H10O5 Deoxyribose of DNA and Ribose of RNA
Hexoses: C6H12O6 Glucose, Fructose, Galactose — use for respiration
Disaccharides: double sugars — two sugar units linked together
Maltose: glucose + glucose — intermediate between glucose and starch
Sucrose: glucose + fructose — food transported in the phloem of plants is a sucrose solution
Lactose: glucose + galactose — the sugar present in milk
Polysaccharides: multisugars — the three examples are multiglucoses
Starch: plant glucose reserve
Glycogen: glucose reserve of animals and fungi. Glycogen stored in skeletal muscle and liver
Cellulose: plant cells walls and fibre in our diet
Dietary Sources of Carbohydrates
Monosaccharides: fruit, honey and jam.
Disaccharides: Sucrose - fruit, table sugar. Lactose - milk. Maltose - germinating seeds.
Polysaccharides: Starch: bread, rice, pasta, potatoes, seeds.
Cellulose: fruit, vegetables, wholegrain cereals, nuts.
Structural Role of Carbohydrate
Cellulose walls of plant cells.
Chitin in the cell walls of fungi.
Metabolic Role of Carbohydrate
Energy Source: energy released by the respiration of glucose is used to make ATP.
Energy Storage: starch in plants, glycogen in animals and fungi.
Lipid
Elements: CHO – with more H but less O than carbohydrates.
Composed of glycerol with three fatty acids linked to the glycerol.
Fat – solid lipid at room temperature. Oil – lipid that is liquid at room temperature.
Phospholipid: two fatty acids and a phosphate group linked to the glycerol.
Good Dietary Sources: meat, milk, butter, cheese, plant oils, margarine.
Structural Role of Lipid
Lipids and Phospholipids are very important in cell membrane structure.
The protective wax cuticle on the outside of leaves.
Metabolic Role of Lipids
Energy storage: more than twice the energy of carbohydrate or protein.
Energy source: released during respiration.
Storage of fat-soluble vitamins.
Some lipids function as hormones.
Hormones as Regulators of Metabolic Activity
Hormones are chemical messengers that cause their target cells or tissues to adjust or alter their activity.
Hormones stimulate or inhibit specific metabolic reactions.
The level of stimulation or inhibition depends on the concentration of hormone in the blood.
Hormones play an important role in homeostasis.
Vitamins
A vitamin is an organic compound needed in small quantities in the diet for health.
Water-soluble Vitamin: Vitamin C (ascorbic acid)
Obtained in fresh fruit and vegetables.
Needed to make and maintain connective tissue and the absorption of iron by the gut.
Long term deficiency of vitamin C causes a disease called scurvy.
Scurvy symptoms: internal bleeding, bruising, bleeding gums, poor healing.
Fat-soluble Vitamin: Vitamin D (calciferol)
Obtained from milk, eggs, liver, fish liver oils and produced in skin exposed to UV light.
It is needed for bone and tooth formation, bone maintenance and the absorption of calcium from the gut.
Long term deficiency cause diseases known as rickets and osteomalacia.
Major deficiency symptoms: late teething and walking, deformed legs and arms, weak bones.
Minerals
Minerals or mineral nutrients are soluble inorganic salts that contain elements essential for metabolism.
Minerals are only needed in small quantities in comparison to protein, carbohydrate and lipid.
Plants obtain their minerals by absorbing them from external ‘water’ — soil water, freshwater and seawater. Animals receive most of their minerals in the food they eat; some from the ‘water’ they drink.
Plant Mineral Requirement (any two)
Calcium: for the middle lamella that ‘glues’ neighbouring plant cell walls.
Magnesium: for the production of chlorophyll so vital for photosynthesis.
Animal Mineral Requirement (any two)
Calcium: formation of teeth and bones.
Iron: formation of haemoglobin so vital for oxygen transport in our blood.
General Role of Minerals in Living Organisms
Construction of Hard Parts: calcium for teeth and bone; nitrogen for chitin in the cell walls of fungi.
Formation of Soft Tissue: nitrogen and sulphur in the protein of muscle tissue.
Maintain Correct Fluid Concentration: sodium chloride role in blood plasma concentration.
Water: H2O
Importance of Water for Organisms
Fluid Component: 90% of cell cytoplasm, 92% of blood plasma, 97% of tissue fluid and lymph.
Multipurpose Solvent: medium for metabolism and transport.
Take Part in Metabolic Reactions
Photosynthesis: water is a raw material in the light stage.
Respiration: aerobic respiration produces water.
Anabolism: water in produced when the subunits of macromolecules link together.
Catabolism: water is used to break the bonds that hold together the subunits of macromolecules.
Movement of Materials through Cell Membranes: diffusion, osmosis and active transport.
Control Cell Shape
Immature plant cell enlarge to mature size and shape as a result of their absorption of water by osmosis.
Opening and closing of the stoma by change in shape of the guard cells by change in their turgor.
Turgor plays an important role in the support of soft plant tissue.
Good Absorber of Heat Energy
A lot of heat energy has to be absorbed to bring about an increase in temperature or vaporisation.
Water as a medium is a temperature-stable which is so important for homeostasis.
Vaporisation of water is an excellent cooling mechanism.
Mandatory Food Tests
Starch
Yellow-brown iodine solution is placed on the food sample.
A blue-black colour indicates that starch is present.
A yellow-brown colour indicates that starch is not present.
Reducing Sugar
E.g., glucose, fructose, maltose, lactose. (Sucrose is a non-reducing sugar).
Add an equal volume of blue Benedict’s Reagent to the food solution.
Heat but do not boil.
A brick-red colour indicates that reducing sugar is present.
A blue colour indicates that reducing sugar is not present.
Control: water – blue colour result.
Lipid
Rub the food onto brown paper.
A translucent stain that does not ‘dry out’ indicates fat is present.
Control: water – stain dries out and the brown paper remains opaque.
Protein
Biuret Test: Add sodium hydroxide solution to the food solution.
Then add a few drops of blue copper sulphate solution.
Shake the contents vigorously.
A purple-violet colour indicates protein is present.
Principles of Ecology
Definitions Ecology: the study of how living organisms interact with each other and with their abiotic environment.
Abiotic Factors: non-living components of the environment.
Habitat: the organism place of residence to which it is adapted.
Population: a group of individuals of the same species living in the same area that interact and interbreed with each other.
Community: interacting populations of different species living in the same area.
Ecosystem: a community of organisms and the habitat’s non-living components.
Biosphere: the global ecosystem - the Earth’s ‘layer of life’.
Environmental Factors Affecting Living Organisms
Biotic Factors: the effect of other living organism of the same or other species.
Abiotic Factors: the effect of non-living items of the organism’s habitat.
Climatic Factors: the effect of the average weather conditions over time, e.g., temperature, rainfall, day length, humidity, wind, atmospheric pressure.
Edaphic Factors: the effect of soil conditions e.g. pH, aeration, porosity, water content, mineral nutrients, humus, soil type.
Aquatic Factors: e.g. wave action, tides, submergence time, exposure time, salinity, oxygen concentration, currents, sedimentation and light quality.
Nutritional Types of Organisms
Producer (Autotroph): makes its own food from inorganic materials.
Photosynthesis: light is the energy source.
Chemosynthesis: energy released by chemical reactions is the energy source.
Consumer (Heterotroph): cannot make food - uses ‘ready-made’ food.
Herbivore: plant eating animal e.g. rabbit, honey bee, green fly.
Carnivore: flesh eating animal e.g. fox, hawk, ladybird.
Omnivore: plant and flesh eating animal e.g. hedge hog, field mouse.
Decomposer: detritus feeder e.g. earthworm, most bacteria and fungi.
Saprophyte: bacterium or fungus that feeds on detritus.
Feeding Relationships
Food Chain: a list of species, each being food for the next species in the list, i.e.
Grass > Rabbit > Fox
Bramble > Aphid > Ladybird > Sparrow > Hawk
Trophic Level: the position of a species in a food chain.
Bramble: first trophic level or primary producer.
Aphid: second trophic level or primary consumer.
Ladybird: third trophic level or secondary consumer.
Sparrow: fourth trophic level or tertiary consumer.
Hawk: fifth trophic lever or quaternary consumer.
Short Food Chains
Inefficiency of energy transfer to the next trophic level.
The energy needs of each organism is about 90% of its food intake.
Almost 90% of an organism’s food is used in respiration.
Food Web A food web is a flow chart showing the feeding connections in a community.
Textbook Diagram: food web diagram.
A food web is made by linking food chains.
The links are food sources used by two or more species.
All species in a community are connected through the food web.
A change in any one species causes changes in all populations.
Pyramid of Numbers
A Pyramid of Numbers is a bar chart showing the number of individuals at each trophic level of a food chain.
Textbook Diagram: normal and inverted pyramids of numbers. The number at each trophic level is influence by:
Energy needs of an individual - the lower the need the great the population.
Mass of an individual - the greater the mass the greater its energy needs.
Energy transfer - only about 10% is transferred to the next level.
Other food sources - the species may be a member of other food chains.
Energy Flow
Textbook Diagram: flow char for energy flow.
About 1% of sunlight energy used for photosynthesis by primary producers.
Each trophic level 90% of the food is used for respiration and lost as heat.
Only about 10% of the food energy is transferred to the next trophic level.
Detritus (dead organic matter) is a very important energy source.
Ecological Cycles
Nutrient Cycling
Textbook Diagram: mineral cycling flow chart.
Carbon dioxide is the source of carbon and oxygen for organic molecules.
Water is the source of hydrogen for biomolecules.
Plants get the other elements as soluble salts from the abiotic environment.
Plants are the direct or indirect source of nutrients for consumers.
Consumers ‘steal’ the materials they need, as food, from other organisms.
Decomposers return the inorganic nutrients to the abiotic environment.
Carbon Cycle
Textbook Diagram: carbon cycle flow chart.
Carbon is the most important element in biomolecules as it forms their skeletal framework.
Nitrogen Cycle
Textbook Diagram: nitrogen cycle flow chart.
Bacteria in the Nitrogen Cycle - how they benefit from their roles in the nitrogen cycle:
Nitrogen Fixing Bacteria: usuable form of nitrogen for biomolecule formation.
Saprophytic Bacteria: receive a supply of materials for energy, growth and reproduction.
Nitrifying Bacteria: produce ATP by the nitrification process.
Denitrifying Bacteria: nitrites and nitrates are their oxygen source for ATP formation.
Biotic Factors
Competition Competition is the rivalry between individuals of the same or different species for the same resources.
Plant Example: grass and daisies compete for light, space, water.
Animal Example: fox and hedgehog compete for food e.g. earthworms.
Competitive Adaptations
Yellow petals of buttercup flower: to win the battle for insect pollinators.
Antibiotics secreted by soil bacterial to inhibit their competitors for nutrients.
Ecological Benefit of Competition
Controls and limits the size of the competitive species.
Maintains a species at a sustainable level.
Competition is a major factor in the evolution.
Important factor in maintaining the ‘balance of nature’ in the community.
Predation Predation is the hunting and killing of one animal by another for food.
Examples: fox killing rabbits; ladybird killing aphids.
Ecological Benefit of Predation
Maintains the prey species at a sustainable level.
Predation is a major factor in the evolution of the prey species.
Predator Adaptations, e.g., fox.
Reddish fur: camouflage to avoid detection by rabbits.
Long canine teeth: to kill the prey and tear flesh from it when feeding.
Great speed: to outrun the prey to capture it.
Prey Adaptations, e.g., rabbit.
Rests underground: predator avoidance.
Long ears: good hearing to detect the predator.
White tail: conspicuous warning signal to other rabbits.
Textbook Diagram: Predator-Prey Graph - Know how to interpret this graph. Symbiosis Symbiosis is the relationship between individuals of two or mores species living together.
Commensalism: symbiosis where one species gains benefit and the other species does not gain but is not at any serious disadvantage. Example: lichens and trees - the lichens gain a place to grow.
Parasitism: symbiosis where one species feeds off and harms the other. Example: lice on hawks.
Mutualism: symbiosis where all species gain. Example: lichens - the fungus gains food from the algae and the algae gain shelter, water plus mineral nutrients from the fungus.
Niche A species niche is everything about how it lives and fits into the community.
Each species in a community has a unique niche.
Human Population
Food supply and disease are the major factors affecting human population.
Great prosperity is a major factor influencing the population of developed countries.
Textbook Diagram: Human Population Graph
The greater the food supply the greater the potential for population growth.
Famine reduces the population - death and/or migration.
Famine is often linked to war - war zones have reduced agricultural activity.
Prosperity leads to population reduction due to a decline in the birth rate.
Convenient, effective and easily available contraception reduces the birth rate.
Disease, especially among infants, often results in a high death rate.
Modern medical practice has massively reduced the death rate from disease.
Modern medicine and absence of contraception has led to hugh population increase in many developing nations.
Human Impact on an Ecosystem
Conservation
Conservation is positive care management of the environment to maintain biodiversity.
Involved Activities:
preservation of ecosystems
restoration of spoilt habitats
balanced use of resources
the safeguarding endangered species
Example of Conservation Practice (only one example required)
Set-aside in Agriculture
Farmland - a commercially managed habitat
Reduced species diversity, low population of native species
Set-aside - agricultural activity suspended in part of the farm
‘Return to nature’ and/or reintroduction of ‘lost’ species
Natural community re-established
Pollution
Pollution is any human activity that contaminates any part of the biosphere with substances that degrade or harm the natural community.
Pollution also threatens
human health
food production
supply of natural raw materials
restricts recreational activities
future generations are denied their right to a wholesome planet
Pollutant: a substance made during human activity in a quantity that harms the natural environment.
Sulphur Dioxide - an example of a pollutant (only one required)
Main Source: fossil fuel burning.
Converted to sulphuric acid in the atmosphere.
Pollution of land and water habitats by ‘acid rain’.
Increased acidity of soil and water - plant and animal life directly inhibited.
Soil Problems - less fertile.
Toxic metal levels increased.
Reduced mineral recycling due to decline in the populations of bacteria and fungi.
Aquatic Habitat Problems
Acidification kills algae and bacteria.
Insect and fish life decline.
Ultimately - lifeless lakes.
Terrestrial Plant Problems
Damages cell membranes and destroys chlorophyll.
Weakens plant’s immune system - greater disease damage.
Human Health Problems
Lung and breathing trouble.
Metal contaminated drinking water can cause nervous system difficulties.
Building Damage
Stonework, mortar and metalwork attacked.
Sulphur Dioxide Control
Burn natural gas instead of coal, oil or peat.
Remove sulphur dioxide before the waste gases are released.
Greater use of renewable energy sources and nuclear power.
Less use of the car - greater use of public transport.
Spread lime - reduces soil and water acidity.
Fossil Fuel Burning - an example of one human polluting activity. <SSH> (only one required)
Acid Rain
sulphur dioxide causes two thirds of the problem
nitrogen oxides causes the remainder of the problem
Carbon Dioxide - suspect in ‘Global Warming’ (enhanced Greenhouse Effect)
Carbon dioxide levels have risen by almost 30% since Industrial Revolution.
Carbon dioxide is a ‘greenhouse gas’.
Atmospheric temperature has been increasing.
Is carbon dioxide a major factor in ‘global warming’.
Suspected effects of ‘global warming’: sea level rise, climate change, increased
desertification, less agricultural land, plant and animal distribution changes.
Smoke: huge mass of tiny carbon particles.
Reduce photosynthesis - less light and blocked stomata.
Human health - lung damage.
Role of Micro-organisms in Pollution Control
Organic Waste (i.e. human sewage and farm slurry.)
Organic waste is food and nutrient source for bacteria and fungi.
Increased use of special ‘fermenters’ for household, district and city waste.
The natural gas produced can be used as an energy source.
Waste reduced to by 98% i.e. 2% of original mass.
Oil Spillage: bacterial decomposition of oil, speed up by inoculating the oil.
Bioremediation: bacteria and fungi can be used to decontaminate soil and groundwater of pesticides, metals and even radioactive materials.
Waste Management
Major Problems
Large volume: domestic (2 mt), agricultural (22 mt), industrial (6 mt) in Ireland. {mt = million tonnes}
Disposal: landfill, recycle, destroy or convert to other uses.
Landfill Difficulties
Local groundwater polluted.
Current sites almost full – strong local protest against new sites.
Incineration Difficulties
Atmospheric pollution - local and regional.
Strong local protest against placing an incinerator in their area.
Possible pollution of ground water.
Waste Minimisation
Much better than waste disposal.
Packaging makes up 50% of domestic waste and is easy to reduce.
New uses for materials previously dealt with as waste e.g. much slurry now use as organic fertiliser; fish waste used as poultry or pig feed; forestry waste now converted to sawdust for processed wood.
Recycle: multiple uses - glass bottles, metal cans, and paper.
Role of Micro-organisms in Waste Management
Breakdown of domestic and agricultural organic waste by bacteria and fungi.
Purposely designed treatment tanks are used for aerobic and anaerobic decay.
Kitchen organic waste can be broken down in a ‘compost bin’ for garden fertiliser.
Ecological Fieldwork: Principles and Practices
Grassland Habitat
Description of Habitat: General Map and/or Photographs taken at different seasons.
Climate: Cold Temperate Oceanic
Grassland Diversity of Living Organisms
Kingdom Monera: bacteria - saprophytic, nitrogen fixing, nitrifying bacteria.
Kingdom Fungi: yeast of leaves, common field mushroom.
Kingdom Protoctista: Amoeba in damp soil, Pleurococcus on rock and tree bark.
Plant Kingdom: grass, daisy, buttercup, dandelion, clover, bramble, oak, ash.
Animal Kingdom: rabbit, fox, aphid, earthworm, sparrow, hawk, mouse, badger.
Microhabitats within the Grassland Habitat Soil, ditch, oak aerial system, hedgerow, stone wall, oak root system.
A study to discover which species are present in the habitat.
The study will also include absence of expected species.
The unexpected presence or absence of species can indicate unusual environmental conditions.
Identification keys, charts, books can be used to name species.
Quantitative Survey A study to measure the distribution, population, frequency or cover of a species.
Display of Results Graphs, histograms, bar charts, pie chart, flow charts and maps can give a much clearer report of the survey results than a long piece of prose.
Local Ecological Issues Related to the Grassland Habitat
Bird and rabbit kills by local domestic cats.
Exotic garden plants colonising the habitat.
Fragmented distribution of daisies and buttercups due to recreational use.
Increased sparrow population due to local bird feeders.
Mandatory Activities
Identification Using a Key
The field key below is a dichotomous key. It is a sequence of pairs of statements only one of a pair applies to the organism you to identify.
1 (a) Animal with backbone 2 (b) Animal without backbone 3
2. (a) Covering of feathers 4 (b) Covering of hair 5
3. (a) Tough hard outer body 6 (b) Soft body 7
4. (a) Red feathers covering upper chest - Robin (b) Large black and white - Magpie
5. (a) Dog-like, long bushy tail - Fox (b) Long ears, short white tail - Rabbit.
6. (a) Three pairs of legs - Insect (b) Four pairs of legs - Spider
7. (a) Segmented body - Earthworm (b) Unsegmented - Slug
Identification Steps for Spider: 1(b), 3 (a), 6 (b).
Description of Earthworm from Key: segmented body, soft, no backbone.
Conduct a Quantitative Survey of Plants, e.g., distribution of daisies
Method: Line Transect (x3)
Set a measuring tape straight across the habitat in the direction of change in an influential environmental factor e.g. soil water, pH, and nitrogen content.
On a map of the habitat mark the trace of tape - this is a line transect.
Walk beside the line and indicate, on the map, the position of each daisy plant touched by the line.
Repeat the process twice more from other start positions.
Combine the results to establish the daisy distribution.
Relate the distribution to the variation of the environmental factors.
A map is an appropriate mode for the display of the results.
Conduct a Quantitative Survey of Animals, e.g., fieldmouse population Day 1
Capture field mice using small mammal traps.
Record the number of captured mice e.g. 20.
Mark each with a dab of red paint on the belly surface.
Release each at their capture site.
Allow time for the mice to readjust to normal conditions.
Day 2
Capture field mice as before.
Record the number captured e.g. 18.
Record the number of recaptures (marked mice) e.g. 6.
Return the mice to the habitat at their capture site.
Calculation: Population = Day 1 Captures x Day 2 Captures Number of Recaptures
= 20 x 18 6
= 60 mice
Change in population over a year is best displayed as a graph.
Determining the Frequency of a Plant Species
Method: many random quadrats e.g. 100.
Randomly pick quadrat sites within the habitat.
At each quadrat record the plant species present.
For each species record the number of quadrats is was found in.
This number is its frequency if a hundred quadrats were used.
Frequency is the percentage occurrence of a species with a large sample of randomly chosen quadrats.
Suitable Quadrat Size: 1/4 m2 (0.25 m2 ).
Frequency is displayed clearly as a bar chart.
Determining the Percentage Cover of Sedentary Species
Textbook Diagram: pin-frame
Method: pin-frame.
Set out a straight transect line across the habitat.
Place the pin-frame beside the line at the start.
Push down each pin, to the ground, and record the species touched.
Move the frame to the next half-metre and repeat.
Record the total number of pins used.
For each species record the number of ‘hits’.
Calculation: Percentage Cover = Number of ‘Hits’ x 100
Total Number of Pins
Percentage cover is the proportion of ground screened or occupied by a species.
Percentage cover is distinctly presented as a pie chart or histogram.
Investigation of Abiotic Factors (Three Mandatory Activities) Soil pH
Air-dry the soil - leave exposed to air until constant mass.
Sprinkle a small pinch of soil onto a white plate.
Add universal indicator solution until soil is quite wet.
Thoroughly mix the soil and the universal indicator.
Press the mixture so some indicator oozes out.
Match the indicator colour to a colour on the pH chart.
The number on the matching colour is the soil pH.
Cowslip and rock rose prefer basic soils. Heather and bilberry prefer acidic soils.
Percentage Soil Water
Using a scales find the mass of an evaporating dish, e.g. 15g.
Find the mass of the dish plus fresh soil, e.g. 55g.
Subtract to calculate the mass of the fresh soil, e.g. 40g.
Dry the soil in an oven at 1008C until constant mass.
Find the mass of the dish plus the dry soil, e.g. 45g.
Mass of Soil Water = (ii) - (v) = 10g.
Calculation: Percentage Soil Water = Mass of Soil Water x 100 Mass of Fresh Soil = 10g x 100 40g
= 25%
The common rush prefers soil with a high percentage of water. Daisies prefer soil of medium water content.
Soil Nitrogen Level
Add 25g of fresh soil to 200cc of salt solution.
Mix thoroughly in a closed bottle.
Filter the soil suspension.
Add four drops of diphenylalamine reagent to one drop of soil filtrate.
Results - Deep Blue: High nitrate content. Pale Blue: Low nitrate content.
Clover is abundant in those areas of low soil nitrate. Grass is abundant in areas of high nitrate level.
Adaptations of Organisms to their Environment
An adaptation is a feature that suits the organism to its environment. Adaptations are solutions to a problem.
Examples of Adaptations (see also competitive, predator and prey adaptations.)
Needle-like mouth parts of aphids tap food from the phloem of the plant.
Ladybird warning colouration: releases toxic fluids to deter predators.
Grass shoot tips are at or below ground: adaptation to survive grazing.
Field mice are nocturnal: predator avoidance.
Collection Methods in Ecological Studies (Mandatory Activity)
Textbook Diagrams of the following:
Small Mammal Trap
Pitfall Trap
Cryptozoic Trap
Pooter
Net: sweep net, insect net, plankton net or fish net.
Tullgren Funnel
Direct search for a particular species is a common practice.
Errors During Fieldwork
Bias: purposely choosing sample sites to get ‘good results’ or avoid work.
Too Few Sample Sites: may not give accurate representative results.
Surveyor Variation: students vary in ability, commitment and interest.
Equipment Quality: measurement and trapping success will be affected.
Changing Nature: results may depend on the time of day, season or year.
Chance: cannot survey every square centimetre so even with many sites some species may be missed.
Improper Trapping Techniques: all evasive species may not be captured and/or insufficient numbers captured in follow up surveying.
The Cell
Cell Theory
All living organisms are made up of cells and new cells are produced when live cells divide.
Textbook Diagrams: animal and plant cell as seen with light and electron microscopes.
Light Microscope Study Components of Animal Cells: cell membrane, cytoplasm, nucleus, chromosomes.
Extra Components of Plant Cells: cell wall, chloroplast, vacuole.
Electron Microscope Study Extra components and details:
Cell membrane, mitochondrion, nuclear pores, ribosomes, chromatin, details of chloroplast mitochondrion structure, double membrane nature of nuclear envelope and outline structure of cell membranes.
(The term protoplasm is useful and refers to the cell membrane, cytoplasm and its contents and the nucleus. The large vacuole of plant cells is not included.)
Cell Structure
Cell Membrane
Semipermeable: water, oxygen and carbon dioxide freely pass through it, many other chemicals cannot.
Selectively permeable: controls entry and exit of specific materials.
Keeps cell contents together allowing efficient coordination of its activity.
Maintains the interior of the cell at a suitable constant composition for efficient metabolism
Cytoplasm
The living contents of a cell excluding the nucleus and large vacuoles.
A complex solution in which the cell’s organelles are suspended.
Many biochemical processes take place here, e.g., glycolysis and fermentation.
About 90% water.
Nucleus
Contains DNA, the hereditary material.
The genes are present in the DNA.
Controls the cell’s structure and metabolism.
DNA (deoxyribonucleic acid) is visible as chromatin in active cells and as chromosomes during mitosis and meiosis.
A nucleus is not present in a red blood cell or phloem sieve element.
Nuclear Pores Large molecules can pass between the cytoplasm and the nucleus through these pores. Examples: RNA from nucleus to cytoplasm and nucleotides from cytoplasm to nucleus.
Chromatin Chromatin is the very fine thread-like combinations of DNA and protein in non-dividing nuclei. The protein assists in the efficient packaging and regulation of DNA activity. A human nucleus contains 46 such fine threads of chromatin.
Chromosomes A chromosome is a ‘condensed chromatin’ thread visible during mitosis and meiosis.
Haploid nuclei have one set of chromosomes i.e. one of each kind of chromosome. Each chromosome has a unique set of genes. Each gene has a specific locus – it is on a particular chromosome at a specific site.
Diploid nuclei have two sets of chromosomes i.e. two of each chromosome.
Symbol for haploid: n Symbol for diploid: 2n
The nuclei of human somatic cells are diploid (2n). Each human nucleus has 46 chromosomes i.e. two sets of 23 chromosomes. One set was received from the mother in the haploid egg cell, the other in the father’s haploid sperm cell.
Sex Chromosomes: the 23 rd pair. Female: XX Male XY
Mitochondria:
The aerobic steps of respiration occur here – Krebs Cycle and Electron Transport System.
36 of the 38 ATPs from one molecule of glucose are produced in the mitochondrion.
Liver, muscle and nerve cells are rich in mitochondria.
Bone and fat cells have low numbers of mitochondria.
Root hair cells and meristematic cells of plants have large numbers of mitochondria.
Stem and root ground tissue cells of plants are low in mitochondria.
Textbook Diagram: detail of mitochondria structure - for recognition purposes only.
Ribosomes:
Composed of RNA and protein.
Function in protein synthesis – translation of mRNA into a specific sequence of amino acids.
Chloroplast
Photosynthesis is the major function of the chloroplast.
The light stage takes place in the green internal membranes.
The dark stage occurs in liquid part of the chloroplast.
Starch may be stored in the chloroplast
Textbook Diagram: detail of chloroplast structure - for recognition purposes only. Large Plant Cell Vacuole
Storage of water, food (sugar, amino acids), ions, wastes.
Role in cell elongation during plant growth.
Plant Cell Wall
Composed of cellulose.
Permeable to water and solutes
Protects and supports plant cells.
Prevents plant cells bursting in more dilute solutions.
The middle lamella of pectin glues neighbouring plant cell walls together.
Structural role – it is the ‘plant skeleton’.
Prokaryotic Cell: no nucleus. Prokaryotic cells do not have membrane-bound organelles such as nuclei, mitochondria or chloroplasts. All prokaryotes are placed in the Kingdom Monera i.e. the bacteria.
Eukaryotic Cell: membrane-bound nucleus is present. Membrane-bound organelles such as nuclei, mitochondria and chloroplasts are only present in eukaryotic cells. The Protista, Fungi, Plants and Animals are eukaryotic organisms.
Cell Continuity (Mitosis and Meiosis)
Cell Continuity
Cell Continuity is the unbroken succession of cells since the evolution of life 3.8 billion years ago.
New cells can only be produced by cell division.
New cells are needed for reproduction, formation of multicellular organisms, and cell replacement.
Cell Cycle
The Cell Cycle is the orderly sequence of events of cell reproduction.
There are three stages of the cell cycle: interphase, division of the nucleus (mitosis or meiosis) and cytokinesis.
1. Interphase The cell grows, proteins are made, increases the number of cytoplasmic organelles, DNA replication.
2. Division of the Nucleus Mitosis: two daughter nuclei, genetically identical the original nucleus, are formed. Meiosis: formation of four haploid genetically different daughter nuclei from the original diploid nucleus.
3. Cytokinesis The cytoplasm divides between the new daughter nuclei. Therefore each nucleus with its allocation of cytoplasm becomes a new cell.
Mitosis
Haploid and diploid nuclei can undergo mitosis.
Haploid (n): one set of chromosomes is present in the nuclei/only one of each different chromosome is present.
Diploid (2n): two sets of chromosomes are present in the nuclei/two of each different chromosome is present.
Role of Mitosis
Formation of a multicellular organism.
Asexual reproduction e.g. Amoeba, yeast and vegetative reproduction of plant.
Cell replacement and regeneration.
Gamete formation in the flowering plant.
Faithful copying of genes and their transfer to the next generation of nuclei or cells.
Maintains the correct chromosome number of somatic cells.
Stages of Mitosis Prophase, Metaphase, Anaphase, Telophase. (Mnemonic - Pour Me Another Tea)
Textbook Diagram: Stages of Mitosis Prophase
chromatin condenses forming chromosomes
each chromosome composed of two identical sister chromatids connected at the centromere
spindle fibres forming
nuclear membrane breaks down towards the end of prophase
Metaphase
chromosomes placed individually along the equatorial plane of the cell
each chromosome is connected to both sides of the cell by spindle fibres attached to the centromeres
Anaphase
separation of sister chromatids, now termed chromosomes
the centromeres spit when the spindle fibres shorten
continued shortening results in two identical sets of chromosomes at opposite sides of the cell
Telophase
each chromosome group becomes a nucleus when a membrane is formed around it
the chromosomes uncoil to chromatin
Definitions
Chromatin: composed of DNA and protein a fine loose disperse state — condenses to form chromosomes.
Chromosomes:
condensed chromatin showing up as a group of short thread-like structures
visible with the light microscope in nuclei during mitosis and meiosis
each different chromosome carries a specific set of genes in linear order at particular loci
Chromatid:
often described as half a chromosome
it is one of two threads of condensed chromatin forming one chromosome
the two threads are connected together at the centromere after DNA replication
the X-shaped chromosomes are present during prophase and metaphase
Centromere: a non-DNA region of a chromosome where sister chromatids are held together and spindle fibres attach.
Meiosis
Meiosis: the visible reduction division of a diploid nucleus forming four haploid genetically different daughter nuclei.
Role of Meiosis
Increases genetic variation in the population – role in evolution
Makes sexual reproduction possible
Gamete formation in animals e.g., man
Spore formation: e.g. flowering plants
Site of Meiosis Humans: testis - forming sperm the haploid male gametes; ovary - forming egg cells, the haploid female gametes.
Flowering plants: anther of the stamen - forming the haploid male spores (microspores), ovule of ovary - forming the haploid female spores (megaspores).
Cancer
Cancer is a harmful mass of multiplying cells that is invading normal tissue.
The cancer cells have the ability to separate from the original cell mass, travel throughout the body and set up new harmful cancerous tumours.
Causes of Cancer (any two)
Environmental Chemicals – cigarette smoke, toxic substances in plants, benzene
Physical Agents – nuclear radiation, X-rays, UV light
Biological Agents – viruses
All cancers result from genetic mutation – disruption of the DNA.
Cell Diversity
Cell Co-operation
Tissue: a group of structurally similar cells carrying out a particular function.
Organ: a group of different tissues working together performing a specific job.
Organ System: a group of different organs operating together carrying out a definite task.
Plant Tissues: dermal, ground, meristematic, vascular (xylem, phloem). Animal Tissues: connective, nervous, adipose, muscular.
Plant Organs: root, stem, leaf. Animal Organs: skin, heart, liver, kidney.
Animal Organ Systems: circulatory, nervous, endocrine, reproductive.
Tissue Culture
This is the growth and multiplication of an undifferentiated cells or specific cell types in a sterile nutritive medium in the lab.
Hormones and other growth factors may also be present to keep the cell dividing and/or bring about differentiation.
Applications of Tissue Culture
Cancer Research: culturing specific type of cancer cell for scientific study.
Plant Breeding: culturing of genetically modified plant cells to produce new variety of food plant.
Movement Through Cell Membranes – Diffusion, Osmosis, Turgor
Diffusion
Diffusion is the net passive movement of particles (atoms, ions or molecules) from a region in which they are in higher concentration to regions of lower concentration. Diffusion stops when the concentration is the same in all regions.
Some major examples of diffusion in biology:
Gas exchange at the alveoli — oxygen from air to blood, carbon dioxide from blood to air.
Gas exchange for photosynthesis — carbon dioxide from air to leaf, oxygen from leaf to air.
Gas exchange for respiration — oxygen from blood to tissue cells, carbon dioxide in opposite direction.
Transfer of transmitter substance — acetylcholine from presynaptic to postsynaptic membrane at a synapse.
Osmosis — diffusion of water through a semipermeable membrane.
High Diffusion Rate: short distance, high temperature, big concentration difference and a low density medium.
Osmosis
Osmosis is a special example of diffusion. It is the diffusion of water through a semipermeable membrane from a more dilute solution to a more concentrated solution.
Note: diffusion and osmosis are passive, i.e. energy from ATP is not used.
A semipermeable membrane is a barrier that permits the passage of some substances but not others; it allows the passage of the solvent molecules but not some of the larger solute molecules.
Cell membranes are described as selectively permeable because not only do they allow the passage of water but also allow the passage of certain solutes. The presence of particular solutes stimulates the membrane to open specific channels or trigger active transport mechanisms to allow the passage of those chemicals across the membrane.
Some major examples of osmosis
Absorption of water by plant roots.
Reabsorption of water by the proximal and distal convoluted tubules of the nephron.
Reabsorption of tissue fluid into the venule ends of the blood capillaries.
Absorption of water by the alimentary canal — stomach, small intestine and the colon.
Osmoregulation Osmoregulation is keeping the concentration of cell cytoplasm or blood at a suitable concentration.
(a) Amoeba, living in freshwater, uses a contractile vacuole to expel the excess water from its cytoplasm. (b) The kidneys maintain the blood at the correct concentration.
Osmosis and Plant Cells (a) Plant Cells in a Less Concentrated Solution
the plant cells gain water by osmosis.
the vacuole and cytoplasm increase in volume.
the cell membrane is pushed harder against the cell wall causing it to stretch a little.
the plant tissue becomes stiffer, it has swollen slightly and has increased in size and mass.
(b) Plant Cells in a More Concentrated Solution
the plant cells lose water by osmosis.
the vacuole and cytoplasm decrease in volume.
the cell shrinks away from the cell wall.
shrinkage stops when the cell sap is at the same concentration as the external solution.
the plant tissue becomes flaccid, it has shrunk slightly and has decreased in size and mass.
Turgor
Turgor is the pressure of the swollen cell contents against the cell wall when the external solution more dilute than the cell sap of the vacuole.
Role of Turgor in Plants
Mechanical support for soft non-woody tissue, e.g., leaves.
Change in shape of guard cells forming the stomatal opening between them.
Enlargement of young immature plant cells to mature size.
Osmosis and Food Preservation
The food is placed in a high salt or sugar medium.
The salt or sugar concentration is higher than the cytoplasm of bacteria or fungi.
Bacteria or fungi, that contaminate the food, will lose water by osmosis and their metabolism will decline.
Many will die but some bacteria may survive by forming dormant resistant endospores.
Meat and fish are often preserved in salt.
Fruit is commonly preserved in sugar as in jam or syrup.
Active Transport
Active transport is the energy demanding transfer of a substance across a cell membrane against its concentration gradient, i.e., from a region where the substance is in lower concentration to where it is in higher concentration.
Special proteins within the cell membrane act as specific protein ‘carriers’. ATP generated by respiration supplies the energy for active transport.
Major Example of Active Transport Reabsorption of glucose, amino acids and salts by the proximal convoluted tubule of the nephron in the kidney.
Mandatory Activity
Demonstration of Osmosis
Tie a knot at one end of about 20 cm length of semipermeable Visking tubing.
Half fill the tubing with a strong sucrose (table sugar) solution.
Seal the open end by tying a knot in it.
Set up a similar tube with tap water.
Measure the mass and ‘stiffness’ of both tubes.
Place both tubes into a beaker of tap water.
Allow to stand for about 30 minutes.
Results: the sucrose tube is has increased in size, is much stifferthe external water has decresed in volume; the tap water tube shows no change.
Conclusion: water passed through the tubing into the sucrose solution by osmosis.
Enzymes
Proteins that function as biological catalysts are called enzymes.
Enzymes speed up specific metabolic reactions.
Low contamination, low temperature and fast metabolism are only possible with enzymes.
Metabolism is fast, with the product made to a high degree of purity.
General Properties
Catalysts
Protein
Specific
Reversible — can catalyse the reaction in both directions
Denatured by high temperature and change in pH
Rate of action affected by temperature and pH
Protein Nature of Enzymes
Composed of C, H, O and N. Sulphur (S) may also be present.
One or more polypetide chains - large number of linked amino acids.
Formed by the ribosomes – translation of mRNA during protein synthesis.
Denatured by high temperature and unfavourable pH.
Folded Shape of Enzymes
The polypeptide chains are folded into a particular three-dimensional shape.
The correct folded shape is essential for enzyme action.
The shape gives the enzyme special domains that function as active sites.
The compatible substrate molecules bind to the active site.
Different enzymes have a differently shaped active site.
Roles of Enzymes in Plants and Animals Enzymes catalyse all metabolic reactions.
Lower the activation energy – the energy input needed to bring about the reaction.
Regulate the thousands of different metabolic reactions in a cell and in the organism.
The activity of a cell is determined by which enzymes are active in the cell at that time.
Cell activity is altered by removing specific enzymes and/or synthesising new enzymes.
Active Site Theory
“Lock and Key Hypothesis and Induced Fit”
The enzyme’s active site has a shape closely complementary to the substrate The substrate locks into the active site of the enzyme.
The active site alters its shape holding the substrate more tightly and straining it.
An enzyme-substrate complex is formed.
The substrate undergoes a chemical change – a new substance, product, is formed.
The product is released from the active site.
The free unaltered active site is ready to receive fresh substrate.
Textbook Diagram: Enzyme Action Sequence.
Native Enzyme: an enzyme that can function normally because its active site has the correct shape.
Denatured Enzyme: an enzyme that cannot operate because the shape of its active site is altered and so the substrate cannot combine with it – change in shape resulting in loss of biological function.
Renatured Enzyme: the denatured enzyme has recovered it shape and function when the temperature and/or pH are again favourable.
Denaturation
Heat is a form of energy. The addition of heat can cause a change in the three-dimensional shape of a protein.
The new shape results in a change in the chemical properties of the protein.
The protein is said to be denatured if the shape change causes it to lose its normal biological activity. Denaturation is not usually reversible.
Some denatured proteins do renature when their normal environmental conditions are restored.
Factors Affecting Enzyme Action
Enzyme action occurs when the enzyme and substrate collide.
During the collision the substrate slots into the active site of the enzyme.
Collisions happen because of the rapid random movement of molecules in liquids.
(i) Temperature
Textbook Graph: Temperature-Enzyme Graph
at 0°C enzyme action is low because the movement of molecules is low
the collision frequency between enzyme and substrate is therefore low
increasing the temperature speed up the movement of molecules
collision frequency increases raising the collision frequency
therefore enzyme action increases
maximum enzyme action at 40°C - maximum collision frequency between native enzymes and substrates
enzyme action decreases above 40°C because the enzymes are denaturing
when all the enzymes are denatured enzyme action stops
(ii) pH
Textbook Graph: pH-Enzyme Graph
enzyme action is greatest within a narrow range of pH, because
all the enzymes are in their native state
increased acidity or alkalinity decreases the ability of the substrates to bind to the active site
and so enzyme action decreases
a major pH change denatures the enzymes so enzyme action stops
Optimum Enzyme Activity Enzymes function best within a narrow range of temperature and pH.
Human intracellular enzymes work best at 37°C and pH 7.
Bioprocessing
Bioprocessing is the use of biological materials (organisms, cells, organelles, enzymes) to carry out manufacturing or treatment prodedures of commercial or scientific interest.
Examples of Bioprocessing with Enzymes:
Glucose Isomerase: production of fructose from glucose.
Sucrase: production of glucose and fructose from sucrose.
Immobilised enzymes are not free in solution – for example they cam be held in a bead of soft permeable gel or coat the internal surface of a porous solid.
Teztbook Diagram: Bioreactor Setup.
Bioprocessing Procedure
Bioprocessing with immobilised enzymes is carried out in a bioreactor.
The gel beads, with the immobilised enzymes, are held in suspension in the nutrient medium.
The bioreactor is sterile – micro-organisms would have a major negative impact.
Temperature, pH, substrate and product concentration and waste level are checked constantly.
The product can be produced by continuous flow or batch processing.
Advantages of Immobilised Enzymes
Easier purification of the product as the separation of the enzyme beads is not a problem.
Easy to recover and recycle the enzymes – more economical process.
The enzymes remain functional for much longer as it is a gentler process.
Mandatory Activities
To Determine the Effect of pH on the Rate of Enzyme Action.
Textbook Diagram: show set up of the apparatus.
Substrate: starch. Enzyme: amylase.
Use the same volume of the same substrate and enzyme solutions.
Temperatrue at 37°C: heated water bath and thermomenter.
Different pH values: use buffer solutions – pH 3, pH 5, pH 7, pH 9, pH 11.
Experiment: starch + buffer + amylase.
Control: starch + buffer + water.
Each minute test a small sample of experiment and control for starch using iodine.
Control Results: no starch break down as blue-black is the constant result.
Experiment Results: record the time at which each first produced a yellow-brown result.
Yellow-brown means starch is not present, therefore starch breakdown occurred.
Calculate rate of enzyme activity: Rate = 1 ???ime
Repeat many times to verify the results.
Graph the results – pH on x-axis.
To Determine the Effect of Temperature on the Rate of Enzyme Action
Substrate: starch. Enzyme: amylase.
Use the same volume of the same substrate and enzyme solutions.
Suitable constant pH: pH 8 – use a buffer solution.
Different Temperatures: 0°C – use ice bath, 20°C – room temperature, use a heated water bath and thermometer for temperatures greater than room temperature (30°C, 40°C, 50°C….)
Experiment: starch + buffer + amylase.>
Control: starch + buffer + water.
Each minute test a small sample of experiment and control for starch using iodine.
Control Results: no starch break down as blue-black is the constant result.
Experiment Results: record the time at which each first produced a yellow-brown result.
Yellow-brown means starch is not present, therefore starch breakdown occurred.
Calculate rate of enzyme activity: Rate = 1 ???time
Repeat many times to verify the results.
Graph the results – temperature on x-axis.
Investigate the Effect of Heat Denaturation on the Activity of an Enzyme
Substrate: starch. Enzyme: amylase.
Use the same volume of the same substrate and enzyme solutions.
Suitable constant pH: pH 8 – use a buffer solution.
Temperatures: 37°C – human body temperature.
Control: starch + buffer + native amylase.
Experiment: starch + buffer + boiled saliva (helded at 100°C for 10 minutes).
Each minute test a small sample of experiment and control for starch using iodine.
Experiment: no starch break down as blue-black is the constant result.
Control: the yellow-brown colour indicates starch breakdown.
Native Amylase: starch breakdown. Denatured Amylase: no breakdown of starch
Conclusion: heat denaturation of the enzyme results in the loss of its catalytic activity.
Repeat many times to verify the results.
Prepare an Enzyme Immobilisation and Examine its Application
Preparation of Immobilised Enzyme
Prepare a solution of calcium chloride.
Mix sodium alginate and amylase solutions.
Draw the mixture into a syringe.
Gently squeeze drops of the mixture into the calcium chloride solution.
Allow the beads of immobilised amylase to harden in the calcium chloride solution.
Collect the beads in a strainer and wash with distilled water.
Examination of the Application of Immobilised Enzyme
Control Jar: amylase solution mixed with a starch solution.
Experiment Jar: immobilised enzyme beads in the same volume of the starch solution.
Temperature: 20°C – room temperature.
Swirl both jars equally.
Every minute test a sample from each for starch using iodine.
Record the time to achieve a yellow-brown colour – starch breakdown completed.
Now test for reducing sugar using Benedict’s Reagent – brick-red colour forms.
Note that it is much easier to remove the immobilised enzyme than the free enzyme from the product solution and the immobilised enzyme beads can be easily reused.
Photosynthesis
Photosynthesis is the production of organic compounds from inorganic molecules using light energy trapped by chlorophyll.
chlorophyll Carbon Dioxide + Water + Light >> Glucose + Oxygen
chlorophyll 6CO2 + 6H2O + Light >> C6H12O6 + 6O2
Location of Chlorophyll in Photosynthetic Plant Cells
Chlorophyll is present in the chloroplasts.
Chlorophyll occurs in the internal green membranes of the chloroplast.
Chloroplasts are ‘the Little Green Slaves of Photosynthetic Plant Cells’.
Textbook Diagram: Chloroplast.
outline of chloroplast structure so it can be recognised as a chloroplast
double outer membrane – inner membrane is smooth, not folded
green internal membranes
Light Stage in the green internal membranes
Dark Stage in the liquid portion of the chloroplast
Source of Light in Leaf Cells
The natural source of light for photosynthesis is the sun.
Artificial light can also be used if it contains red and/or blue wavelengths of visible light.
Source of Carbon Dioxide in Leaf Cells
Carbon dioxide in air is the major source.
Carbon dioxide produced by the mitochondria during aerobic respiration is a minor source.
Carbon dioxide dissolved in water is the major source for aquatic plants.
Source of Water in Leaf Cells
Water from the soil is the major source. Delivered to the leaves in xylem tissue.
Some water is also produced by the mitochondria of leaf cells during aerobic respiration.
Role of Photosynthesis in the Biosphere
Source of food for plants.
Source of oxygen for aerobic respiration of plants, animals and aerobic micro-organisms.
Direct source of food for herbivores and omnivores.
Indirect food source for carnivores and decomposers.
Original organic source from which fossil fuels formed.
Oxygen and Photosynthesis
In normal conditions photosynthesis is much faster than aerobic respiration.
Oxygen formation by photosynthesis is far greater than that used by respiration.
The excess oxygen is released from the plant to the atmosphere.
Oxygen produced by photosynthesis = oxygen used in respiration + oxygen released into air.
General Outline of Photosynthesis
Light Stage
Light energy used to make ATP.
Light energy used to produce NADPH from NADP+.
Oxygen gas as a by-product.
Half of the water used as a hydrogen source is recycled
Dark Stage
Carbon dioxide and hydrogen are used to make carbohydrate.
The energy to drive this process comes from ATP.
An outline of the Biochemistry of Photosynthesis
Light energy is absorbed by chlorophyll.
Absorbed light energy causes the emission of energised electrons.
Some of these electrons can release their energy in a controlled fashion synthesising ATP.
Other electrons are carried into the Dark Stage.
The absorbed light energy is also responsible for the break up of water.
The break up of water releases oxygen, electrons and protons (H+, hydrogen ions).
The oxygen passes from the chloroplast, some will be used by the mitochondria for aerobic respiration and the remainder will be passed into the atmosphere.
The electrons from water run to chlorophyll releasing energy forming ATP.
The protons are released into the ‘pool of protons’ in the chloroplast.
In the Dark Stage electrons from chlorophyll, protons from the pool and carbon dioxide react together forming carbohydrate
Detailed Description of Photosynthesis
The Light Phase or Light-Dependent Stage (only takes place in the presence of light)
Cyclic Electron Transport – Pathway 1.
Non-cyclic Electron Transport – Pathway 2.
Cyclic Electron Transport
Light energy is absorbed by chlorophyll in the green internal membranes of the chloroplast.
An ‘excitable’ electron in chlorophyll absorbs light energy.
This electron is elevated to a higher energy level.
The energised electron escapes the chlorophyll molecule.
An electron acceptor molecule picks up this energised electron.
The electron is passed along an ‘electron carrier system’ where its ‘excess’ energy is released.
The excess energy is used to produce ATP by the phosphorylation of ADP.
The electron then returns to chlorophyll after all the excess energy has been given off.
Non-cyclic Electron Transport
Light energy is absorbed by chlorophyll in the green internal membranes of the chloroplast.
An ‘excitable’ electron in chlorophyll absorbs light energy.
This electron is elevated to a higher energy level.
The energised excited electron escapes form the chlorophyll molecule.
An electron acceptor picks up this energised electron.
The electron acceptor passes this electron to NADP+ becoming NADP (neutral).
NADP then receives another electron becoming NADP-.
NADP- now attracts a hydrogen ion (H+) or proton from the proton pool in the chloroplast.
NADP- now becomes NADPH.
The loss of electrons from chlorophyll causes the break up of water.
Water breaks up into oxygen, protons (hydrogen ions) and electrons.
The oxygen passes out of the chloroplast by diffusion.
The protons pass into the general pool of protons in the chloroplast.
The electrons pass to chlorophyll as replacement for those lost to NADP-.
The electrons from water pass through an electron transport chain resulting in ATP formation.
The Dark Stage
The Light Independent Phase
Does not require light.
Occurs in light and also in darkness as long as the products of the light phase are still available.
The dark stage runs if ATP, NADPH and carbon dioxide are present.
Takes place in the liquid portion of the chloroplast.
Carbohydrate is the crucial product of the dark stage.
ADP, P and NADP+ are recycled for use in the light stage.
Details of Pathway
CO2 diffuses into the chloroplast from the mitochondria or from the external environment.
NADPH delivers electrons and a proton to CO2 (NADP ? NADP+ + 2e- + H+)
Electrons, protons and carbon dioxide combine to form carbohydrate [Cx (H2O)y] e.g. glucose.
The energy needed for this reaction is supplied by the break up of ATP.
NADP+, ADP and P pass back to the light stage.
NADP+
NADP+: nicotinamide adenine dinucleotide phosphate
Function: to transfer energy for the formation of complex organic compounds.
The energy is in the form of energy-rich electrons.
In photosynthesis these electrons came from light activated chlorophyll.
NADP+ becomes NADPH in the light stage.
NADPH transfer electrons and protons to carbon dioxide reducing it to carbohydrate.
NADP- is regenerated when NADPH passes on the electrons and proton.
Promoting Crop Growth in Greenhouses
Artificial Lighting
Increase the light intensity to increase the rate of photosynthesis
Increase the light duration to increase the total amount of photosynthesis.
Increase Carbon Dioxide Concentration:
Raises the rate of photosynthesis so more food produced.
Carbon dioxide enrichment is achieved by gas cylinders or kerosene burners.
Mandatory Activity
To Investigate the Influence of Light Intensity on the Rate of Photosynthesis
Textbook Diagram: set up of the investigation.
Place a funnel over Elodea, pondweed, in a beaker of pond water at 25°C.
The funnel is raised off the bottom on pieces of blue-tack. This allows continuous free diffusion of CO2 to Elodea.
Invert a test tube full of water over the stem of the funnel to collect any gas from the Elodea.
Place the beaker on a hot plate at 25°C.
Maintain and monitor the temperature of the water with a thermometer.
Excess sodium bicarbonate is placed in the water to give a constant saturated solution of CO2.
Place the lamp (the only light source) at a predetermined distance from the plant.
Use a light meter to measure the light intensity at this distance. Record the light intensity.
Allow the plant five minutes to adjust to the new conditions.
Count the number of oxygen bubbles given off by the plant in a five-minute period.
Repeat the count twice more and calculate the average of the three readings. This is the rate of photosynthesis at that particular light intensity.
The gas should be checked to prove that it is indeed oxygen — it relights a glowing splint.
Repeat at different light intensities by moving the lamp to different distances.
Run a control: identical set up but at a constant light intensity.
Result: no change in the rate of photosynthesis.
Conclusion: change in light intensity causes a change in the rate of photosynthesis.
Graph the results placing light intensity on the x-axis.
Note: make sure you know the shape of this graph and are able to interpret it.
Respiration
Respiration is the enzymatic-controlled release of energy from organic compounds in a living cell.
Definitions
Aerobic Respiration The enzymatic-controlled release of energy from organic compounds using free molecular oxygen.
Anaerobic Respiration The enzymatic-controlled release of energy from organic compounds in a living cell using substances other than free molecular oxygen as electron acceptors.
Fermentation The enzymatic controlled release of energy form organic compounds yielding simpler organic compounds.
The energy released by respiration is of very little value unless it is used to produce ATP.
ATP Adenosine triphosphate (ATP) is the most abundant short-term energy store and immediate source of energy for cell work.
ATP: adenine + ribose sugar + three phosphate groups |
Adenine + Riboseis called Adenosine |
ATP = A + P + P + P |
A: adenosine P: phosphate |
ATP releases energy when the last phosphate is removed |
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A + P + P + P ATP |
|
A + P + P + energy + P (free) ADP + energy + P (free) |
ADP: adenosine diphosphate |
ATP can be remade by the addition of a phosphate onto ADP, i.e., by the phosphorylation of ADP. The phosphorylation of ADP requires energy. Respiration is one source of energy to produce ATP.
Living cells use up ATP at a very fast rate — a human cell needs about 2 million a second. In order to maintain constant energy, a supply of ATP must be replaced as it is used.
Note: Light is the energy source to make ATP in the light dependent stage of photosynthesis. ATP is made during pathway 1 and pathway 2 of the light stage. The ATP from the light stage is used to drive the dark phase reactions in the production of glucose.
Aerobic Respiration: Glucose + Oxygen ? Carbon Dioxide + Water + Energy (38 ATP) C6H12O6 + 6O2 ? 6CO2 + 6 H2O + Energy (38 ATP)
Fermentation Plants and Fungi: Glucose ? 2 Ethanol + 2 Carbon Dioxide + Energy (2 ATP) Animals and some Bacteria: Glucose ? 2 Lactic Acid + Energy (2 ATP)
Lactic acid is a colourless liquid miscible with water.
In fermentation the glucose is only partially broken down. A lot of energy is still available in ethanol and lactic acid.
Note: ethanol is one member of the family of chemicals called the alcohols; ethanol is the alcohol of beer, wine and spirits.
(Anaerobic respiration is incorrectly known as fermentation.) Aerobe: an organism that lives and grows only in the presence of free oxygen; it respires aerobically.
Anaerobe: an organism that can live and grow in the absence of free oxygen, it can produce ATP without free oxygen.
Obligate Anaerobe: an organism that is not capable of aerobic respiration (free oxygen is toxic to some of these).
Facultative Anaerobe: an organism that is usually respires aerobically but can survive by anaerobic respiration in the absence or shortage of free oxygen.
Aerobic Respiration of Glucose (6C)
Stage 1: Glycolysis
Takes place in the cytosol – the non-organelle part of the cytoplasm.
Oxygen not used and its presence not required.
Net production of 2ATPs.
Two pairs of hydrogen atoms are ‘donated’ to NAD+.
The six carbon glucose is converted to two pyruvates.
Pyruvate is a three carbon compound.
A compled enzyme pathway is involved in glycolysis.
Stage 2. Formation of acetyl co-enzyme A Takes place in the mitochondrion – the presence of free oxygen is essential.
Pyruvate enters the mitochondrion.
Pyruvate loses a carbon dioxide and a pair of hydrogen atoms.
Pyruvate is thus converted to an two carbon acetyl group.
Co-enzyme A links to the acteyl group forming acetyl coenzyme A.
Krebs Cycle
Acetyl co-enzyme A combines with a four carbon compound in the mitochondrion.
A six carbon is formed with the release of co-enzyme A.
Loss of two carbon dioxides and pairs of hydrogen regenerates the four carbon compound.
One ATP is produced for each turn of the Krebs cycle.
The hydrogen pairs become involved in the Electron Transport System.
Electron Transport Chain
NAD+ is the hydrogen acceptor.
NAD+ takes a hydrogen pair forming NADH + H+.
The H+ (hydrogen ion or proton) enters into solution.
NADH passes two electrons to the Electron Transport Chain in the mitochondrion.
The electrons travel to oxygen releasing energy which is used to make ATP.
About three ATPs are produced for each pair of electrons.
At the end of the chain electrons, oxygen and hydrogen ions from solution form water.
Aerobic Respiration of Glucose – ATP Account
Glycolysis: 2 ATPs
Krebs Cycle: 2 ATPs
Electron Transport Chain: 34 ATPs
Total: 38 ATPs.
NAD+
NAD+ is a hydrogen acceptor – it takes on electrons and hydrogen ions.
NAD+ transfers the electrons and hydrogen ions to other substances in certain cellular activities.
NAD+ collects electrons from many diverse sources and passes them on to electron transport chains.
As the electrons pass along the electron transport chain ATP is synthesised.
Fermentation
The enzymatic controlled release of energy form organic compounds yielding simpler organic compounds and does not involve electron transport.
The two pairs of hydrogen removed from glucose during glycolysis are donated to pyruvate, one pair to each pyruvate.
Pyruvate + 2H ? Lactic Acid (animals, some bacteria) - Lactic Acid Fermentation Pyruvate + 2H ? Ethanol + Carbon Dioxide (plants, fungi and some bacteria) - Alcoholic Fermentation.
Advantages of Fermentation
Permits survival of some organisms in oxygen deficient environments.
Supply of extra ATP when the aerobic system cannot meet the demand for ATP
Disadvantages of Fermentation
The organic end products (lactic acid, ethanol) are toxic.
Inefficient: only 2 ATPs per glucose - much chemical remains in the organic end products.
Role of Micro-organisms in Industrial Fermentation
Industrial fermentation: the growing micro-organisms in a liquid medium under any conditions.
There are a wide variety of micro-organisms with a very extensive range of organic compounds of value to us.
Culturing of specific micro-organisms in carefully controlled favourable conditions can yield a rich harvest of important and useful organic substances – ethanol, acetone, lactic acid (cheese, yoghurt), ethanoic acid (vinegar), antibiotics, vitamins, amino acids, insecticides, enzymes, citric acid, carbon dioxide and methane (natural gas).
Bioprocessing With Immobilised Cells
Bioprocessing is the use of biological materials (organisms, cells, organelles, enzymes) to carry out manufacturing or treatment prodedures of commercial or scientific interest.
Immobilised cells are not free in solution – for example they cam be held in a bead of soft permeable gel or coat the internal surface of a porous solid.
Teztbook Diagram: Bioreactor setup.
Bioprocessing Procedure
Bioprocessing with immobilised cells is carried out in a bioreactor.
The gel beads, with the immobilised cells, are held in suspension in the nutrient medium.
The bioreactor is sterile – other types of micro-organisms would have a major negative impact.
Temperature, pH, substrate and product concentration and waste level are checked constantly.
The product can be produced by continuous flow or batch processing.
Industrial fermentation of alcohol is often carried out with yeast cells immobilised in jel beads.
A yeast suspension is mixed with a sodium alginate solution.
Drops of the mixture are allowed to harden in calcium chloride solution.
Small gel beads with live, trapped yeast are formed.
Nutrients can diffuse through the gel to the live yeast.
Fermentation product will diffuse from the yeast into the liquid medium.
Advantages of Immobilised Cells
Easier purification of the product as the separation of the cell beads is not a problem.
Easy to recover and recycle the cells– more economical process..
The cells remain functional for much longer as it is a gentler process.
Mandatory Activity
Prepare and Show the Production of Alcohol by Yeast.
Boil water for 15 minutes: removes all the dissolved oxygen.
Almost fill two flasks with the deoxygenated water.
Allow them to cool to 25°C in the sealed flasks.
Sealed to prevent re-oxygenation.
Dissolve glucose in each flask.
Measure the density (specific gravity) of each solution using a hydrometer and record.
Add live yeast to one — the experiment.
No yeast in the other — the control.
Place a thin layer of oil on the top of the water in each.
The oil keeps the water out of contact with the air and prevents reoxygenation
Insert a ‘fermentation lock’ into each.
The fermentaton lock allows waste carbon dioxide to escape without the entry of air.
Maintain the temperature at 25°C in a water bath or on a heating tray.
After a week test each flask density and for alcohol using orange acidified potassium dichromate.
Results: Control: no change in density and no alcohol (no colour change) Experiment: the density of the solution has decreased and colour change from orange to green
Conclusion Yeast fermentation produces alcohol.
DNA - Structure, Replication, Profiling and Screening
DNA Structure
DNA - deoxyribonucleic acid
DNA is the genetic material of all living cells and many viruses.DNA Structure P P SA = TS P P SC ? GS P P ST = AS P: phosphate S: deoxyribose (5C) sugar Nitrogenous Bases A: adenine T: thymine G: guanine C: cytosine P + S + Base = Nucleotide Nucleotide: subunit of DNA. Adenine and guanine are purines bases Thymine and cytosine are pyrimidines bases
Must have a minimum of three pairs of bases in the diagram. Hydrogen bonds link the complementary base pairs. Two between A and T. Three between G and C.
The structure of DNA: an alpha double helix of two polynucleotide strands.
The genetic code is the sequence of bases on one of the strands.
A gene is a specific sequence of bases which has the information for the formation of a particular protein.
DNA is self-replicating — it can make an identical copy of itself.
Replication allows the genetic information to pass faithfully to the next generation.
Replication occurs during interphase just before mitosis and meiosis.
The chromosomes contain most of the cell’s DNA.
DNA is present in mitochondria and chloroplasts.
Textbook Diagram: molecular structure of DNA.
The genetic information is held within the base sequence along a DNA strand.
A gene is a specific section of a DNA strand that contains the information for a particular protein or polypeptide.
Coding Structures
These are the parts of the DNA that contain vital information for the synthesis of Protein or RNA.
These coding sequences are present within genes.
Non-coding Structures.
These are the parts of the DNA that do not contain critical information for the synthesis of protein or RNA.
The non-coding sequences are found between genes and within genes.
These non-coding sequences have been termed ‘junk DNA’ but they do play a role in gene expression, act as spacer material, permit the synthesis of many new proteins and play an important role in evolution.
Non-coding DNA makes up 95% of human DNA.
Non-coding DNA within genes are called introns.
DNA Replication
Replication means to make a perfect identical copy.
Nucleotides are synthesised in huge quantity in the cytoplasm.
An enzyme unzips the two complementary strands of DNA.
New complementary nucleotides link to the exposed bases on the separated strands.
A new complementary strand is built along each ‘old’ strand.
Two DNAs, identical to the original and each other, are now present.
Each DNA is ‘half old’ and ‘half new’.
Textbook Diagram: DNA replication.
DNA Profiling
Introduction
Popularly known as DNA fingerprinting.
Produces a unique pattern from an individual’s DNA which can then be used to distinguish that individual form another.
Extremely variable regions of non-coding DNA are used.
Genetically different individuals produce different profiles.
The closer the genetic relationship between individuals the more similar their profiles.
Process of DNA Profiling Four Major Steps:
Extraction of DNA: the cells of an uncontaminated biological sample (blood, semen, hair root, cheek cell) are broken open and the DNA is released and separated.
Digestion: special enzymes are used to cut the DNA at specific point and produce a set of fragments of varying lengths.
Separation: the fragment mixture is placed in a block of gel and separated by gel electrophoresis on the basis of size – the smaller the fragment the further it travels.
Highlighting the Fragment Pattern: a radioactive genetic probe, which by binding to complementary DNA, shows up the positions of the DNA fragments on X-ray film as dark bands.The positions of these bands are the genetic profile of the individual and the more numerous the bands the more reliable the ‘fingerprint’.
Applications of DNA Profiling
Genetic Screening: detection of inherited diseases.
Parenthood Disputes: establishing
Crime Investigation: rape, murder or was the suspect at the scene of the crime.
Animal Pedigree Check
Archaeological: check relationship between human remains in archaeological sites and people alive today.
DNA (Genetic) Screening
Genetic screening is a test to determine if an individual carries an abnormal gene for a particular trait.
Genetic screening can also tell if the individual is homozygous normal, homozygous abnormal or heterozygous.
Special genetic probes or DNA profiling may be used in genetic screening.
RNA
RNA - ribonucleic acid
Three different types of RNA, (messenger, ribosomal, transfer) and all are involved in protein synthesis.
mRNA: copies the information from the DNA.
rRNA: each ribosome is composed of roughly equal parts RNA and protein.
tRNA: carries the specific amino acids to the mRNA in contact with the ribosome.
Some RNA molecules can function as catalysts.
Differences between DNA and RNA
DNA is a double polynucleotide strand; RNA is a single polynucleotide strand.
DNA contains the sugar deoxyribose; RNA contains the sugar ribose.
DNA has thymine base but not uracil; RNA has uracil base but not thymine.
DNA is self-replicating, RNA is copied from the DNA so it is not self-replicating.
Mandatory Activity
Isolation of DNA from Plant Tissue Textbook Diagram: DNA isolation from plant tissue.
Make up a salt and detergent solution in water.
The detergent breaks up the cell membranes setting free the chromatin.
The salt protects the DNA from the phosphates of the cell membranes.
Mash a small piece of fresh onion with a glass rod in a beaker.
The mashing breaks the plant cell walls releasing the chromatin into the liquid.
Decant the liquid, containing the chromatin, from the pulp into a clean test tube.
Add a protease to the liquid. The protease digests the protein of the chromatin freeing the DNA.
Slowly pour freezer-cold ethanol into the test tube and let it stand for a short time.
A cold ethanol forms a separate layer on top of the DNA solution.
DNA is insoluble in ethanol and so it precipitates out at the boundary as fine whitish threads.
At the boundary twirl the roughly scratched end of a glass rod or twirl a small wire loop.
A sticky gel-like material is collected – this is DNA.
Protein Synthesis and Genetic Engineering
Gene
A definite section of DNA containing a particular sequence of bases that codes for a specific protein.
Protein Synthesis
The transcription of a specific DNA base sequence and its translation, by a ribosome, into a particular amino acid sequence forming a definite protein.
Genetic Code
The system that determines the function of each possible triplet sequence of the mRNA.
Most triplets specify a particular amino acid.
Some triplets function as a start or stop signal for protein synthesis.
It is a degenerate code as a particular amino acid may be determined by more than one triplet.
Process of Protein Synthesis – transcription and translation
Transcription – DNA base sequence to mRNA base sequence
The ‘code’ for the protein is carried by one of the DNA strands in the gene.
An enzyme separates the two DNA strands at the gene locus exposing the gene sequence.
A complementary chemical copy (mRNA) is made of the gene sequence – new nucleotides, following the base pair rule form a complementary RNA strand against the DNA gene sequence strand – the enzyme RNA polymerase links the new nucleotides forming mRNA.
Uracil is the complementary base to adenine in RNA, thymine is not present in RNA.
The complementary RNA copy is called messenger RNA (mRNA).
The mRNA separates from the DNA strand and passes from the nucleus to the cytoplasm.
Translation – mRNA base sequence to amino acid sequence.
Ribosome subunits bind to the start point of the mRNA.
A ribosome is now formed at the start point of the mRNA.
The ribosome will ‘decode’ the mRNA in sets of three bases (triplets).
Each triplet specifies a particular amino acid.
The sequence of triplets on the mRNA determines the sequence of amino acids.
Two triplets of the mRNA are in contact with the mRNA.
Two complementary tRNA attach to these two mRNA triplets.
The amino acids of the tRNA bond together.
The leading tRNA detaches from its amino acid and from the mRNA.
The ribosome ‘moves’ to the next triplet and another complementary tRNA attaches.
The newly arrived complementary tRNA then adds a new amino acid.
The process repeats, triplet by triplet, to the end of the mRNA (until a stop triplet is reached).
The amino acid sequence is now complete.
The polypeptide (amino acid chain) folds giving the protein its normal functional shape.
Ribosomal RNA (rRNA) A ribosome is almost 50% protein and 50% RNA.
The RNA molecules in ribosomes are called ribosomal RNA (rRNA).
Transfer RNA (tRNA) tRNA is soluble RNA in the cytoplasm.
Single stranded but folded back on itself with three exposed bases (triplet) at one end and a particular amino acid at the opposite end.
tRNAs are ‘adapters’ linking amino acids to nucleic acids in protein synthesis.
Note: transcription occurs in the nucleus; translation occurs in the cytoplasm.
Note: triplets on the mRNA are called codons; the exposed triplet on the tRNA is called an anticodon.
Note: start point triplet on mRNA is AUG; stop point triplets on mRNA are UAA, UGA or UAG.
Genetic Engineering
Genetic engineering is the manipulation and alteration of genes in basic and applied research.
Gene manipulation involves isolating specific genes and transferring them to organisms of the same or different species.
Gene alteration involves altering the base sequence of a specific gene leading to a modification of the normal protein with possible new advantageous properties.
Gene cloning is the production of many working copies of a specific gene by inserting it into a host cell which will undergo continuous cell division.
Gene manufacture is carried out by special ‘machines’ that can synthesise DNA to any desired base sequence – can produce the gene for specific proteins is their amino acid sequence is known or can make novel genes.
Applications of Genetic Engineering
Transgenic Micro-organism Example: Recombinant bacteria containing the human insulin gene are used to produce insulin to treat diabetes.
Transgenic Plant Example: Bacterial gene inserted into the DNA of certain crop plants to make them resistant to a specific herbicide. The herbicide kills the weeds but not the crop plant. The intention is to reduce the quantity of herbicide by making its use more effective.
Transgenic Animal Example: A particular human blood-clotting factor is extracted from the milk of genetically modified sheep. The clotting protein is needed to treat a form of haemophilia.
Gene Cloning
Human Insulin - an example of genetic engineering.
Textbook Diagram: production of human protein by genetically modified bacteria.
Isolation
Human DNA containing the insulin gene is isolated from human cells.
Plasmid DNA is isolated from bacteria.
Cutting
A specific restriction enzyme cuts the plasmid DNA and the human DNA at specific sites.
The cut plasmid DNA and cut human DNA are mixed.
Transformation – uptake of foreign DNA by cells
Human DNA fragments containing the gene binds to the cut ends of the plasmids – ligation.
Recombinant plasmids containing a human gene and its control sequence have been formed.
Bacteria are cultured in a medium rich in the recombinant plasmid.
Some bacteria take up the recombinant plasmid.
The genetically modified bacteria are harvested separately and cultured.
The human insulin gene is copied when the plasmids replicate.
Expression
The human insulin gene is ‘active’ and its specific protein is being synthesised by the host cell.
Insulin protein is harvested from the bacterial culture.
It is the ‘manufactured’ human insulin gene that is now used to produce insulin by genetic engineering.
Genetics
Definitions
Genetics: The science of heredity and variation.
Chromosome: Condensed chromatin showing up as a short thread-like structure in nuclei during mitosis and meiosis, carries a specific set of genes in linear order at particular loci.
Diploid: Nucleus or cell containing two sets of chromosomes, i.e., two of each different chromosome.
Haploid: Nucleus or cell containing one set of chromosomes, i.e., one of each different chromosome.
Homologous Chromosomes: Chromosomes that pair at meiosis, have the same length and banding pattern plus carrying the same genes at the same loci, i.e., they have the same sequence of genes.
Gene: A specific section of DNA or chromosome that has the information for a particular characteristic.
Allele: An alternative form of a gene, e.g., the gene for height in pea plants has two forms (i) Tall (T) and (ii) Small (t).
Locus: The position of a gene on its specific chromosome, i.e., the gene’s address.
Dominance: The allele that is expressed totally in the homozygous and heterozygous condition.
Recessive: The allele that is only expressed in the homozygous condition, it is not expressed at all in the heterozygous.
Genotype: The genetic make up of the organism or the pair of genes governing each trait under study in the individual.
Phenotype: The observable features of the individual determined by the interaction of the genotype and environment.
Homozygous: The pair of genes controlling the characteristic are identical alleles, e.g., TT or tt.
Heterozygous: The pair of genes controlling the characteristic are different alleles, e.g., Tt or CrCw.
Heterozygous Dominant: The pair of alleles controlling the trait are different alleles one being dominant over the other, e.g., Tt.
Incomplete Dominance: Two different alleles are equally dominant and the heterozygous genotype produces an intermediate phenotype between the two respective homozygous genotypes, e.g., coat colour in horses, Red (Cr) and White (Cw) and the heterozygous CrCw is a roan colour horse.
Sex Chromosomes (heterosomes): The chromosome pair which determines the gender of the individual; in humans the twenty third pair, females are XX and males are XY.
Autosomes: The non-sex chromosomes or somatic chromosomes, they do not determine the individual’s gender.
Sex-linked Genes or Sex linkage: Genes or traits whose controlling genes are on the X sex chromosome but not on the Y sex chromosome so the recessive phenotype occurs more often in males than in females.
Linkage or Gene linkage: Genes, controlling different traits, on the same chromosome have a tendency to be inherited together, they tend not to undergo independent assortment.
Mutation: An inheritable change in the genotype of an organism.
Mendel’s First Law: The Law of Segregation Every characteristic is governed by a pair of factors which separate at gamete formation such that each gamete only receives one of the pair. At fertilisation a pair of factors is re-established for each characteristic. Memory Trick: 212.
Mendel’s Second Law: Law of Independent Assortment (The Law of ‘Free Mixing’) During the formation of gametes the distribution of the genetic factors for two or more traits is completely random; each pair of factors segregates freely so all combinations of alleles for the different genes are equally likely.
Genetic Variation
Meiosis Independent assortment of the homologous chromosomes generates great genetic variation among the daughter nuclei (cells).
Crossing-over generated even more variation.
Sexual Reproduction If the gametes are produced by meiosis then all the gametes will be genetically different.
Random fertilisations between the gametes of two individuals hugely enhance the genetic variation of the offspring.
Mutation
Somatic mutations that occur in the body cells are not passed on by sexual reproduction to the next generation.
Somatic mutations in plant can be transferred by vegetative propagation.
Germinal mutations occurring in the cells that give rise to gametes can be transferred to the next generation.
Most mutations are disadvantageous and will not persist.
Mutations are the major method by which new genetic information enters a species.
Gene mutations involve change in the base sequence of a gene which will disrupt the amino acid sequence of the protein and possible the shape plus performance of the protein e.g. sickle cell anaemia caused by one incorrect base in the entire sequence.
Chromosome mutation can involve a change in the number and sequence of genes in a chromosome or change in the number of chromosomes e.g. Down’s Syndrome is caused mostly by the inheritance of three of chromosome number 21 instead of two copies.
The natural mutation rate can be increased by certain environmental factors e.g. UV light, nuclear radiation, X-rays, chemicals in cigarette smoke and certain food preservatives.
Non-nuclear Inheritance
DNA is also present in mitochondria and chloroplasts.
Mitochondria and chloroplasts reproduce by binary fission involving replication of their DNA.
Male gametes do not pass on mitochondria or chloroplasts to the zygote at fertilisation.
Mitochondria and chloroplasts are inherited from the parent that contributed the egg cell.
In humans, the inheritance of mitochondrial DNA is along the female line.
Parkinson’s disease, certain muscular and neurological disorders are attributed to mitochondrial DNA mutations.
Genetics Crosses
Monohybrid: the inheritance of one characteristic, e.g., the height of pea plant, seed shape. Dihybrid: the inheritance of two different characteristics.
Mendelian Characteristic The gene controlling the characteristic has only two alleles, one being dominant over the other. Examples: height of pea plant — two alleles, Tall (T) dominant and small (t) recessive. Shape of pea seed — two alleles, Round (R) dominant and wrinkled (r) recessive. Possible genotypes: TT = tall; Tt = tall; tt = small. RR = Round; Rr = Round; rr = wrinkled.
Crosses Which Led Mendel to his Discovery of his Two Laws of Inheritance
|
Monohybrid |
Dihybrid |
P1 Phenotypes |
Pure Tall x Pure Small |
Pure Tall Round x Pure Small Wrinkled |
|
|
|
F1 Phenotypes |
Tall |
Tall Round |
F1 Tall x F1 Tall (Selfing) F1 Tall Round x F1 Tall Round |
||
F2 Phenotypes |
Tall : Small |
Tall Round: Tall Wrinkled: Small Round: Small Wrinkled |
|
|
|
F2 Phenotype Ratio |
3 : 1 |
9 : 3 : 3 : 1 |
Calculating or explaining the results of a Genetics Cross Clear understanding of genetics terms is necessary to be able to determine the genotypes of the parents. If numerical results are given, convert these to a ratio and immediately you can determine the possible genotypes of the parents. Follow a particular set of steps in the calculation. The ‘calculation’ is considered to be a diagram so label each level of the work.
|
The Classic Crosses: Numerical Results |
Ratio |
Parent Genotypes |
1. |
67 Tall: |
all Tall |
TT x tt; TT x Tt. |
2. |
95 Tall, 29 Small |
3 : 1 |
Tt x Tt |
3. |
74 Tall, 79 Small |
1 : 1 |
Tt x tt |
4. |
45 Red, 88 Pink, 47 White |
1 : 2 : 1 |
FRFW x FRFW Rr x Rr (incomplete dominance) |
5. |
Red Eye Female 88 White Eye Female 0 Red Eye Male 42 White Eye Male 47 |
gender difference no white eye females |
Sex Linked Gene Rr x R- Female x male |
6. |
Blood Group A x Blood Group B Combine the results of all four crosses. |
Four Possible Crosses |
AA x BB, AA x Bo, Ao x BB, Ao x Bo. |
7. |
953 Tall Round |
all Tall Round |
TTRR x ttrr |
8. |
1842 Tall Round, 597 Tall Wrinkled, 612 Small Round, 204 Small Wrinkled (non-linked: genes are on different chromosomes) |
9 : 3 : 3 : 1 |
TtRr x TtRr |
9. |
763 Tall Round, 756 Tall Wrinkled, 731 Small Round, 766 Small Wrinkled |
1:1:1:1 |
TtRr x ttrr |
10. |
Grey Normal 100, Black Twisted 99, Grey Twisted 11, Black Twisted 9 |
1:1 + 1:1 |
Linked Genes |
Because the behaviour of chromosomes during meiosis parallels Mendel’s Laws then the inheritance ‘factors’ must be present on the chromosomes — the chromosomes contain the genes. |
|||
Method of Calculation 1. Parent Phenotypes 2. Parent Genotypes 3. Meiosis 4. Gamete Genotypes 5. All Possible Random Fertilisations ‘Punnet Square’ 6. Progeny Genotypes 7. Progeny Phenotypes 8. Phenotype Ratio |
Be careful
There is a potential problem with which symbols to use in incomplete dominance.
The gene for flower colour in snapdragons has two alleles which are equally dominant.
One allele has the information for red flower — symbol R or FR.
The other allele has the information for white flower — symbol r or FW.
If you use R and r you must remember that it is incomplete dominance and the genotype Rr is pink not red.
When carrying out sex-linked crosses use chromosome diagrams, label each chromosome X or Y.
Mark with a dot on the X sex chromosome the locus of the gene.
XNXn x XNY — is not a chromosome diagram.
Evolution
Evolution is the change in the characteristics of a population over time; it may also result in the formation of new species.
Evolution by Natural Selection
This theory was put forward by Alfred Russel Wallace and Charles Darwin.
There is great genetic variation within each population.
Population size remains constant even though organisms produce many offspring.
Therefore severe competition for limited resources takes place —‘survival of the fittest’.
The individuals with the best-adapted genetically determined characteristics survive.
New competition – contest to produce offspring.
The better-adapted individuals produce more offspring than the less well adapted.
The next generation is genetically closer to the better adapted individuals of the previous generation.
With each generation the population becomes better adapted to its environment.
Evidence for Evolution
Comparative Anatomy is the study of the structural similarities and differences of living organisms.
Many structures, which appear quite different, have been shown to have the same basic design.
Structures that are different yet similar are said to be homologous. The pentadactyl limb of four-limbed vertebrates is an example.
Modifications of the basic design include:
bat wing for flying
whale fin for swimming
horse leg for running
human arm for grasping
The examples above indicate that they descended from a common ancestor.
Textbook Diagram: human skeleton - to study the bone sequence in the human arm.
Classification – The Five Kingdom System Classification
The great diversity of living organisms is organised into groups that share important biological characteristics such as structure.
The evolutionary connection between organisms becomes clear by this method of classification.
The Five Kingdoms
Monera (Prokaryotae)
Protista (Protoctista)
Fungi
Plantae
Animalia
Kingdom Monera
All the prokaryotic organisms are in this Kingdom.
Cells do not have a membrane bound nucleus.
Cells do not have mitochondria.
Chloroplasts are never present.
All are unicellular and microscopic.
Common Name: Bacteria.
Kingdom Protista
The eukaryotic organisms that are not fungi, plants or animals are placed in this kingdom.
Protists include unicellular, colonial and simple multicellular eukaryotes.
Members include the protozoa, algae and moulds.
Amoeba is a protist.
Kingdom Fungi
The fungi are heterotrophic eukaryotes with cell walls of chitin.
The hypha, a tubular filament, is the basic unit of organisation of many fungi.
The total mass of hyphae is called the mycelium.
Yeast, moulds and mushrooms are fungi.
Kingdom Plantae
The eukaryotic organisms with cell walls of cellulose are plants.
All are multicellular photosynthetic autotrophs.
Plants show a high degree of structural differentiation.
The flowering plants are the most evolved members of this kingdom.
Mosses, ferns and conifers also belong to this kingdom.
Kingdom Animalia
Multicellular, heterotrophic, eukaryotic and cells without a surrounding wall.
Therefore our species belongs to the Kingdom Animalia.
Flowering Plants
Flowers hold the sexual organs of flowering plants.
Flowering plants reproduce sexually by forming seeds in a mature ovary (fruit).
Flowering plants have specialised vascular tissue (xylem, phloem).
The flowering plants are divided into two classes, monocotyledons and dicotyledons.
Monocots and Dicots
Monocoyledons
Plant embryo has one leaf (cotyledon – seed leaf).
Foliage leaves have parallel veins.
Vascular bundles of the stem are scattered or arranged in two or more rings.
Flower parts in three or multiples of three.
90% are herbaceous (non-woody).
Examples: grass, onion.
Dicotyledons
Plant embryo has two leaves.
Foliage leaves have branching veins.
Vascular bundles of the stem are in one ring.
Flower parts in four or five.
Approximately 50% are herbaceous and 50% woody.
Examples: buttercup, pea, oak, ash.
Bacteria
Classification: unicellular prokaryotes of the Kingdom Monera.
Distribution: ubiquitous – found everywhere in the biosphere.
Textbook Diagram: the three major shapes of bacterial cells – spherical, rod, spiral.
Textbook Diagram: detailed structure of bacterium cell.
Structure of Bacterium Cell
Size: about 1,000 smaller than a human cell.
Cell Wall: non-cellulose, supports, gives shape to and protects the cell from bursting when turgid.
Capsule: protection against other micro-organisms and host defences; attachment to solid surfaces.
Flagellum: locomotion.
Genetic Material: single circular DNA molecule with very little attached protein (not a true chromosome), not surrounded by a membrane so not a true nucleus.
Plasmid: small circular DNA – may be one or many present, replicates independently of ‘bacterial chromosome’, may contain genes of use to the bacterium e.g. antibiotic resistance, easily taken up from external environment or transferred from other bacteria.
Reproduction
Method: asexual by binary fission.
Textbook Diagram: sequence showing binary fission.
Bacterium cell is growing.
DNA replicates.
DNA copies separate as bacterium cell grows.
Cross wall forms, between the identical DNA copies, by ingrowth of cell membrane and cell wall.
Two identical daughter cells formed.
Speed: 20 minutes – more than one billion bacteria after 30 generations in 10 hours.
Favourable mutations become established in bacterial populations.
Bacterial populations can evolve very rapidly in response to changes in environmental conditions.
Endospores
Some bacteria form resistant endospores at the onset of extremely unfavourable environmental conditions.
Growth stops, tough wall forms around the dry shrunken cytoplasm, cell ruptures releasing the endospore.
Converts back rapidly to a vegetative bacterial cell when favourable growth conditions return.
Nutrition
Autotrophic: capable of making their own food from inorganic materials.
Photosynthetic: light energy is used to make carbohydrate from carbon dioxide; e.g. green sulphur bacteria.
Chemosynthetic: energy for carbohydrate formation is obtained from chemical reactions; nitrifying bacteria.
Heterotrophic: not able to make their own food from inorganic materials.
Saprophytic: feed on dead organic matter e.g. bacteria of decay, psueudomonas.
Parasitic: live with and feed off another living organism causing it harm e.g. cholera bacterium.
Mutualistic: lives with another living organism from which it receives food but contribute positivel to their partner e.g. symbiotic nitrogen-fixing bacteria in the roots of clover and beans.
Growth Factors
Temperature: affects the rate of enzyme action and excessive heat denatures the enzymes.
Oxygen Concentration
Aerobes: capable of using and growing in air at normal, 21%, oxygen concentration.
Microaerophiles: can survive and use free oxygen but only in low concentration.
Anaerobes: cannot use free oxygen for respiration.
Obligate Anaerobes are killed by free oxygen.
Aerotolerant Anaerobes: can survive free oxygen but cannot use it.
pH: affects the rate of enzyme action; pH wide of optimum denatures the enzymes.
External Solute Concentration High external concentration will cause bacteria to lose water by osmosis slowing or halting metabolism resulting in death and in some will stimulate endospore formation. The cytoplasm of bacteria is usually at a higher concentration than the external environment so water will tend to move into the bacteria by osmosis.
Pressure Pressure lowers the melting point, raises the boiling point and alters the solvent ability of water. Each type of bacterium operates best at the pressure of the ecosystem it evolved in.
Growth Curves
Batch Processing
Textbook Diagram: growth curve of five stages.
Lag Phase: low multiplication rate, bacteria adapting to the new nutrient environment.
Log Phase: rapid metabolism, favourable environmental conditions, fast reproduction.
Stationary Phase: ‘birth’ and ‘death’ rates are equal; growth and reproduction has slowed due to build up of toxins and/or increased competition for nutrients, oxygen, space.
Decline Phase: death rate is greater than reproduction rate; conditions deteriorating.
Death or Survival: bacteria die or survive by going dormant or forming endospores.
Continuous Flow Processing
Textbook Diagram: growth curve graph – constant favourable rate of product formation.
Constant supply of nutrient into the bioreactor at optimum conditions.
Constant removal of culture rich in the product and low in contamination.
Beneficial Bacteria (any two)
Medical: production of antibiotics, hormone and vaccines.
Food Production: cheese, yoghurt, vinegar.
Our Health: mutualistic bacteria in our large intestine – vitamins B and D.
Pollution Control: sewage treatment, bioremediation of polluted environments.
Harmful Bacteria (any two)
Tooth Decay
Food Spoilage
Human Diseases: tuberculosis, pneumonia, cholera, whooping cough, ulcers, tetanus.
Agriculture: livestock and crop diseases.
A pathogen is a disease causing organism.
Pathogenic bacteria cause harm to the host organism they have invaded and are growing within.
Antibiotics
An antibiotic is a chemical substance produced by bacteria or fungi that inhibit the growth of other bacteria or fungi.
The natural role of antibiotics is to inhibit the growth of competing micro-organisms.
Antibiotics used in medicine are harmful to the infectious bacterium/fungus but relatively harmless to us.
Abuse of Antibiotics in Medicine (3P)
Poor Patient Practice: patients stop their course of antibiotics when they feel better – it is essential to complete the course to reduce the risk of antibiotic resistant stains of pathogens developing.
Poor Prescribing Practice: the use of antibiotics for viral infections or as a placebo; antibiotics are ineffective against viruses.
Acquired Resistance to Antibiotics
Initially a type of bacteria may be sensitive to a particular antibiotic.
The bacteria can become resistant if the antibiotic becomes a normal factor in its environment.
Resistance to the antibiotic can be acquired by mutation or uptake of genes from plasmids, viruses or from other resistant bacteria.
Antibiotic resistant strains have the advantage over antibiotic sensitive strains in environments where antibiotics are a constant factor.
Fungi
Characteristics: eukaryotic, heterotrophic, cell wall of chitin.
Distribution: mostly terrestrial, living in soil; some can be found in freshwater and a few are marine.
Nutrition
Saprophytic: feed on dead organic matter e.g. Rhizopus.
Parasitic: live with and feed off another living organism causing it harm, e.g., potato blight fungus.
Rhizopus
Vegetative Structure Textbook Diagram: vegetative structure.
Hypha: a tubular filament growing at its tip, new hyphae form by branching.
Mycelium: all the hyphae together making up the vegetative mass of the fungus.
Stolon Hyphae: horizontal hyphae growing across and colonising the food environment.
Rhizoidal Hyphae: penetrate the solid medium anchoring the fungus.
Sporangium: a vessel in which the spores are formed and are released for wind dispersal.
Sporangiophore: a hypha carrying a sporangium.
Columnella: a cross wall separating the spores from the sporangiophore, aids spore release.
Apophysis: a swelling beneath the sporangium.
Spores: unicellular asexual reproductive and dispersal agents.
Mode of Nutrition
Hyphae secrete digestive enzymes into the external environment.
External digestion of complex biomolecules.
Absorption of the simple soluble products of digestion by diffusion and active transport.
Distribution of absorbed nutrients through the mycelium.
Reproduction and Life Cycle of Rhizopus
Asexual Reproduction
Vegetative structure is haploid (n).
Sporangia form at the tip of sporangiophores.
The sporangium fills with haploid nuclei and cytoplasm.
The columnella forms separating the sporangium from the sporangiophore.
Each nucleus with cytoplasm forms a haploid spore with a tough resistant wall.
The spores are wind dispersed.
The spores germinate forming a new haploid mycelium if conditions are suitable.
Sexual Reproduction Textbook Diagram: sexual reproduction by Rhizopus.
Mycelia of opposite strain are close.
Hyphae of opposite strain grow towards each other.
The touching tips of the hyphae fill with nuclei and cytoplasm – progametangia formed.
A cross wall forms behind each tip forming gametangia.
The hypha behind each gametangium is called a suspensor.
The contents of the gametangia mix.
The nuclei of opposite strains fuse in pairs – fertilisation.
The combined gametangia develop into a diploid zygospore.
The zygospore is thick-walled resistant and dormant.
In favourable conditions the zygospore germinates by meiosis.
A haploid sporangiophore with a spore-filled sporangium grows from the zygospore.
The spores are wind dispersed and germinate forming a new haploid mycelim.
Yeast – a unicellular fungus
Textbook Diagram: the yeast cell.
Reproduction Textbook Diagram: budding of yeast.
Asexual reproduction by budding.
Good growth conditions – cell increasing in size.
A small bubble-like extension grows from the cell.
The nucleus undergoes mitosis.
A daughter nucleus moves into the bud.
The bud may remain attached and form a small colony by further budding.
The bud may detach and undergo budding.
Budding is a very fast method of reproduction.
Economic Importance of Fungi
Beneficial
Alcohol (ethanol) formation for beer, wine and spirits.
Carbon dioxide gas formation for baking and fizzy drinks.
Harmful
Crop diseases, e.g., potato blight.
Food spoilage.
Edible and Poisonous Fungi
What are commonly called mushrooms and toadstools are the reproductive organs of certain fungi.
Scientifically there is no difference between mushrooms and toadstools.
There are no features that distinguish edible from poisonous fungi.
The ability to recognise the handful of deadly types is essential.
Identification of the good edible types is a safe starting point.
Edible Examples: Field Mushroom, Parasol Mushroom.
Poisonous Examples: Death Cap, Fly Agaric.
Mandatory Activity
Investigate the Growth of Leaf Yeast
Three sterile malt agar plates.
Plate 1: control – keep closed and place upside down.
Plate 2: remove lid and place base upside down to prevent its contamination.
Put a ridge of petroleum jelly on the inside of the lid.
Place an ash leaflet with its upper side stuck to the petroleum jelly.
Lift the base of the plate onto the lid and set the plate with the lid on top for a day.
Seal the lid to the base with tape.
After a day turn the plate upside down and incubate.
Plate 3: repeat as for plate 2 but the lower side of the leaflet is in contact with the jelly.
Results: Control Plate: must be clear, without any growth of micro-organisms, in order to continue. Experimental Plates: pink shiny pimples are colonies of yeast.
Compare exposed upper and lower leaf surfaces for yeast distribution.
Precautions
Laboratory Procedures When Handling Micro-organisms
Assume all micro-organisms are harmful.
Swab the laboratory bench with disinfectant t before and after the experiment.
Wash your hands before and after with a disinfectant soap.
Sterilise all equipment, in a pressure cooker, before and after the experiment.
Sterilise the tip of scissors and forceps by flaming immediately before and after use.
Label each plate on its base with an indelible marker pen.
View the incubated plates through the clear lid - never remove the lid.
Sterile all cultures in a pressure cooker before disposal.
Never put anything near or into your mouth in the laboratory.
Never handle items that may have come in contact with cultured micro-organisms.
Sterility: treated so that there are no living micro-organisms.
Asepsis: methods of preventing contamination by unwanted micro-organisms.