Topic 5 Notes

2 Describe the structure of chloroplasts in relation to their role in photosynthesis. Double membrane called the chloroplast envelope Thylakoid - Interconnected membrane bound sacs. Membrane is the site of the Light Dependent reactions. Photosystems - Within membrane of thylakoid, used to capture light energy Stroma - Matrix like fluid of the chloroplast. Enzymes, sugars, organic acids and oil droplets within. Site of Light Independent Reactions Grana - Stacks of thylakoids, forming penny like towers. Chlorophyll - Pigment within chloroplast, attached to photosystems, used for the Light Dependent reactions (provides electrons used for ETC)

3 Describe the overall reaction of photosynthesis as requiring energy from light to split apart the strong bonds in water molecules, storing the hydrogen in a fuel (glucose) by combining it with carbon dioxide and releasing oxygen into the atmosphere. Requires energy in the form of ATP (active process) Light energy used to break hydrogen bonds in water molecules This releases oxygen Energy is stored in glucose until plants release it by respiration 6CO2 + 6H2O (+ energy) -> C6H12O6 + 6O2 4 Describe the light-dependent reactions of photosynthesis including how light energy is trapped by exciting electrons in chlorophyll and the role of these electrons in generating ATP, and reducing NADP in photophosphorylation and producing oxygen through photolysis of water. Light energy excites 2 e in the chlorophyll molecules of PSII to a higher energy level When the 2 es reach their ground state, they are passed along the ETC via a series of redox reactions The energy released from the 2es movement from one electron carrier to the next results, in protons being pumped across the membrane via chemiosmosis This sets up a concentration gradient of H+ ions across the membrane (more H+ in intermembrane space) The flow of H+ into ATP synthase molecule phosphorylates ATP from ADP and Pi 2 es reach PSI and are used to reduce NADP to NADPH2 Water molecule is split by light energy (photolysis) to form 2 es, to replace the ones lost via the ETC, to 2 H+ to reduce another NADP to NADPH2 O2 is also released into the atmosphere to form O2.

Cyclic phosphorylation More NADPH produced, as electrons from PSI is passed to electron carriers to be used in PSII. ATP is formed, and electrons return to PSI Non-cyclic phosphorylation - Electrons from PSI, pass on to an electron carrier to reduce NADP to NADPH

5 Describe how phosphorylation of ADP requires energy and how hydrolysis of ATP provides an immediate supply of energy for biological processes. Phosphorylation - Adding a phosphate to a molecule Hydrolysis - Adding water to split up another molecule (removing a phosphate) ADP and Pi and energy (via ATP synthase) gives ATP This is phosphorylation ATP is an energy storage molecule it can be rapidly hydrolysed (via ATPase) The breaking of the P-P bond releases energy This energy generates ADP and Pi Energy from hydrolysis of ATP used for metabolic processes Used for muscle contraction, active transport, respiration, photosynthesis 6 Describe the light-independent reactions as reduction of carbon dioxide using the products of the light-dependent reactions (carbon fixation in the Calvin cycle, the role of GP, GALP, RuBP and RUBISCO) and describe the products as simple sugars that are used by plants, animals and other organisms in respiration and the synthesis of new biological molecules (including polysaccharides, amino acids, lipids and nucleic acids).

Products of Light Dependent are 4ATP, 2NADPH CO2 (1C) joins to RuBP (5C) with the co enzyme RUBSICO [This forms a 6C unstable intermediate] Breaks down to form two molecules of GP (each 3C) These are reduced by NADPH2 (which is oxidised to NADP) This is also phosphorylated (by the hydrolysis of ATP) This forms 2 molecules of GALP (3C) 2 molecules of GALP (6C in total) can be used to generate one molecule of glucose Cycle can be repeated to generate more molecules of GALP These can be used to generate polysaccharides, amino acids, lipids and nucleic acids RuBP is regenerated after the synthesis of GALP Five out of six molecules of GALP are used for the regeneration of RuBP ATP is hydrolysed to form RuBP This can recombine with CO2 to start the cycle again

7 Carry out calculations of net primary productivity and explain the relationship between gross primary productivity, net primary productivity and plant respiration. Gross Primary Productivity - The rate at which energy is incorporated into producers Net Primary productivity - The rate at which energy taken in by producers is incorporated into new plant biomass and is available for the next trophic level Plant Respiration - The energy taken in by producers which is released through metabolic processes (heat given off) GPP= NPP + R NPP=GPP-R R= GPP-NPP Units is kJ m-2 year-1 GPP could be high because High temperatures High rate of photosynthesis High CO2 levels High light intensity

8 Calculate the efficiency of energy transfers between trophic levels. Energy enters the ecosystem through photosynthesis Some of this Energy is incorporated into producers (plants) A food chain develops as each trophic level of consumers eat other consumers Food chains and food webs show how energy can be transferred through an ecosystem Food chains shows lines of transfer whereas food webs show how many food chains can overlap Organic matter that cannot be eaten that contains energy (e.g faeces and bone) are taken up by decomposers Decomposers will break down this material in detritus and release CO2 into the atmosphere Not all energy is transferred to the next energy level Sun (all available energy) Producer Sunlight may carry the wrong wavelength Sunlight may be reflected off the leaf Sunlight hits parts of the plant which do not photosynthesise Some light passes straight through the leaves Producer Consumer Parts of food e.g bones and roots are not eaten Some parts of food are indigestible and are excreted as waste

9 Discuss how understanding the carbon cycle can lead to methods to reduce atmospheric levels of carbon dioxide (including the use of biofuels and reforestation). In Carbon cycle, CO2 from the atmosphere is taken up by plants for photosynthesis This is converted into organic Carbon molecules, which is eaten by animals and passed along food chains Animals excret inorganic Carbon When animals and plants die, they decay and decompose via decomposers which eat detritus and respire CO2 into the atmosphere Carbon escapes into the soil via fossilisation Carbon in ocean can be incorporated into shells of organisms Some CO2 from the atmosphere dissolves in oceans through diffusion Fossil fuels are burnt for anthropogenic activity via combustion releasing CO2 Carbon sinks are reservoirs of Carbon that have been stored for an indefinite period of time These can be found in oceans and land These were once separate from the carbon cycle and are now exploited by humans (e.g. Fossil fuel usage) Biofuels can be used to reduce atmospheric levels of CO2 These are fuels made from plant based sources. The production and burning of these fuels are carbon neutral Carbon neutral means that there is no or little significance difference between the level of carbon emitted into the atmosphere and the level of carbon taken up by plants Reforestation is the planting of new trees to replace the ones lost This restores the carbon neutrality and carbon offsetting Plants take up CO2 for photosynthesis Non edible sources are favoured because they do not affect food supply Biofuels are also cheaper 10 Explain that the numbers and distribution of organisms in a habitat are controlled by biotic and abiotic factors. Biotic factors - Living features of an ecosystem Abiotic factors - Nonliving features of an ecosystem

Biotic Abiotic

PredationLight

CompetitionOxygen availability

DiseaseTemperature

TerritorySoil: moisture content and pH

Biotic factors1. Predation - Populations of predators are directly linked to the populations of prey. (positively correlated)2. Interspecific competition - Different species compete to occupy one particular niche in a habitat. This means resources for both populations are reduced, so less energy will be available for growth and reproduction, decreasing the populations of both species. 3. Intraspecific competition - Individuals of the same species compete for resources. Both populations compete for the same resources, which then becomes limited, so as a result the population begins to decline. As the population gets smaller, there is less competition for resources as the population get smaller, population grows again. 4. Territory - Area defended by a particular population of organisms to make sure breeding pair has sufficient resources to raise their young. 5. Parasitism and disease - Diseased animals are weakened and may not reproduce successfully. Sick predators may not be able to hunt well. Diseased prey animals are more likely to be caught. Parasites and disease will spread more quickly when there is a high population density. Higher biodiversity means disease will have less effect on the community as a whole.

Abiotic factors 1. Light Intensity - Affects rate of photosynthesis in plants. This can affect their growth and hence, the population available for animals to eat. 2. Temperature - Affects the rate of reaction with enzyme controlled reactions (such as hatching of eggs) If optimum temp, less energy is used up to maintain their core body temp. More energy for growth and reproduction. Population will increase

3. Water availability - Affected by the amount of precipitation, rate of evaporation and edaphic factors. Unless organisms have adaptation for water supply, organisms can die without water supply. 4. Edaphic factors - Structure of soil affect plant populations ( Sand is loose, less prone to waterlogging and light, loam is ideal and heavier, less prone to leaching) Leaching is when water passes through quickly draining soil of minerals needed by plants.

11 Describe how to carry out a study on the ecology of a habitat to produce valid and reliable data (including the use of quadrats and transects to assess abundance and distribution of organisms and the measurement of abiotic factors, eg solar energy input, climate, topography, oxygen availability and edaphic factors). Measuring abundance of organisms in a habitat: Choose a small area within a particular area to investigate Samples picked by random (avoids bias) Use random number generator for coordinates. Place a quadrat (frame or point) at the random coordinates Number of individuals in a species is counted in each quadrat Repeat process to take many samples (to make more reliable data for a valid conclusion) Obtain average from data to work out individuals for the whole area. Multiply by the size of the whole area . Percentage cover can be estimated by taking the average of all samples.

Measuring distribution of organisms in a habitat Select a small area within a particular area to investigate Set up a transect a. Line Tape measure placed along transect and species touching transect are recordedb. Belt Data collected using frame quadrats net to each other along a transectc. Interrupted Tale measurements from quadrat at separate intervals along transect (every other 2m) Number of individuals are counted in each quadrat

Repeat process to take many samples (to make more reliable data for a valid conclusion) Obtain average from data to work out individuals for the whole area. Multiply by the size of the whole area . Percentage cover can be estimated by taking the average of all samples.Types of samplingSystematic --> taken at fixed intervals. Used for observing change of conditions in habitatRandom --> every possible sample has an equal chance of selection

Measurement of Abiotic factors 1. Climate Temp is measured with a thermometer. Rainfall is measured with a rain gauge. Vol. of water collected is measured. Humidity measured with an electronic hygrometer. 2. Oxygen availability - Measure in aquatic habitats. Oxygen sensor for vol of O2 dissolved in water 3. Solar input - Light sensor 4. Edaphic factors - pH measured with indicator fluid. Change in colour compared with pH chart. Moisture content measured using difference in mass before and after drying out a sample in oven5. Topography - Relief - taking height readings using GPS at different points. Slope angle - Clinometer. Aspect - using compass.

12 Explain how the concept of niche accounts for distribution and abundance of organisms in a habitat. Organisms exist in a habitat where the conditions are suitable for their role in a habitat (including its abiotic and biotic interactions) Each species has an unique niche to occupy (e.g. hunting at night in trees, dormant at night) When populations of 2 different species occupy the same niche, this leads to interspecific competition This is because both species are using up the same resources (food and space), so there will not be enough for both species This means that eventually the population of both will decrease due to lack of food resources, so less energy available for reproduction and growth Eventually one species will outcompete and the other species will decrease When two populations of the same species occupy the same niche, this is called intraspecific competition. At first there is a decrease as the resources are being used up by both populations so it becomes limiting

Eventually the population begins to grow again, as there is a smaller population so there is less competition for space and food. This means there is more energy for growth and reproduction.

13 Describe the concept of succession to a climax community. Ecological succession is the process by which an ecosystem changes over time. Biotic conditions change as the abiotic conditions change. Succession occurs in seral stages

PRIMARY1. Pioneer species (e.g Lichens) colonise on land surface. Abiotic conditions are harsh and the pioneer species changes them. When they die and decompose they form the first layer of soil.2. Less hostile conditions (soil more likely to retain water) lead to mosses forming on top of the first layer of soil and changing the abiotic conditions again, making them less hostile. 3. Over time, more layers of soil are formed from the decay of species forming more layers of soil, becoming more saturated with nutrients and water (less hostile) 4. Larger plants and shrubs begin to grow, increasing biodiversity. 5. Trees grow and eventually outcompete smaller plants6. Forms a stable climax community.

Climax Community - Most advanced community that an ecosystem can support. Primary Succession No previous community in area before, only newly formed or exposed. Secondary Succession Previous community occupied before but cleared of plants, nutrient rich soil already formed. Different communities have different climax communities due to differences in climate Succession can prevented by human activity, therefore affecting the outcome of the climax community. This is called a plagioclimax.

14 Outline the causes of global warming including the role of greenhouse gases (carbon dioxide and methane, CH4 ) in the greenhouse effect. Greenhouse effect is not caused by Global warming In the greenhouse effect, light energy from the Sun hits the surface of the Earth Some of the energy is absorbed by the Earth Some of the energy escapes into Space as infrared radiation A small amount of infrared radiation is trapped and reflected from the Earths surface This causes the Earths global temperature to rise An increase in the concentration of greenhouse gases in the atmosphere increases the Earths global temperature Less Carbon Dioxide is used by photosynthesis This is Global Warming Greenhouse gases include, Methane, CO2, water vapour, O3 and Nitrous Oxides Anthropogenic activity (human activity) increases the concentration of Greenhouse gases in the atmosphere This increases the effects of Global warming

15 Describe the effects of global warming (rising temperature, changing rainfall patterns and seasonal cycles) on plants and animals (distribution of species, development and life cycles).

1. Rising Temperature Increase in enzyme activity to optimum temp (until optimum where it decreases) Distribution of species - Will change environmental conditions for some species forcing them to move habitat Development & Life Cycles - Metabolic rate will increase, so life cycle will be quicker. If conditions are too high, metabolic rate will decrease, causing the life cycle to be shorter2. Changing rainfall patterns Distribution of species - If less rainfall is present, can lead to species that are not adapted to living in that environment to move or die out. Development & Life Cycles - Will affect length of dormancy of animals. Will affect length of seasons (drier summers)

3. Seasonal Cycles Distribution of species - Can affect the migration of animals and production of insects and flowering Development & Life Cycles - Will affect hatching rate

16 Explain the effect of increasing temperature on the rate of enzyme activity in plants, animals and micro-organisms. Enzymes Biological catalysts which increase the rate of reaction by lowering the activation energy Increase in temperature (optimum) Increases the amount of kinetic energy in enzyme and substrate More successful collisions, therefore more enzyme-substrate complexes formed

In plants animals and microorganisms Life cycles Increase in temp, increases rate of reaction quicker metabolic rates quicker life cycles quicker hatching rates Temperature above (optimum) Denatures enzymes Some animals cannot hatch Quick life cycles

17 Describe how to investigate the effects of temperature on the development of organisms (eg seedling growth rate, brine shrimp hatch rates). Brine Shrimp hatch rates Set up water baths at a range of temperatures (0, 10, 20, 30 ,40, 50) Control the number of eggs in each beaker - 10 Place 10 each in beakers at temperatures for 2 days Record the number hatched every 5 hours Control the vol of water in each beaker/salinity/oxygen Number of hatches/ hours = rate

Seedling growth rate Measure the height of seedlings in soil tray Incubate seeds at different temperatures Control water content, light intensity, CO2 concentration, incubation period Measure change in heights Change in height/incubation period = rate

18 Analyse and interpret different types of evidence for global warming and its causes (including records of carbon dioxide levels, temperature records, pollen in peat bogs and dendrochronology) recognising correlations and causal relationships. Evidence for Global warming include Ice cores, Temperature records, Pollen in peat bogs and dendrochronology Ice cores contain layers of compressed snow and air bubbles of CO2. This can be used to measure CO2 concentration over long periods of time Temperature records can be recorded from using a thermometer in different geographical regions. Often shows fluctuations but shows the change in temp over time Early records are not reliable Innaccurate equipment and records only collected ina few places Modern records are more reliable as they have data logging equipment Allows more numbers of readings to be taken from many places around the world Pollen in peat bogs can give an indication to climate in regions. Pollen grains are resistant to decay. The species of pollen within peat can determine climate within different time periods. Peat forms when plant material dies but does not decompose Lower layers are the oldest Measuring traces of carbon-14 can be used to establish age of layers Dendrochronology is the study of tree rings. Each year, an outer ring is formed. The thickness of the ring can give an indication as to the climate present in a certain time period and amount of growth (warmer = thicker ring)

19 Describe that data can be extrapolated to make predictions, that these are used in models of future global warming, and that these models have limitations. Climate change models can be used to make predictions about future global warming This can be formed from extrapolation of data (prediction of trends of data for the future) Problem is that there is not enough true understanding of the factors and variables surrounding global warming, so not all conclusions can be fully valid Another problem is the further we predict into the future, the more uncertainties arise

20 Discuss the way in which scientific conclusions about controversial issues, such as what actions should be taken to reduce global warming or the degree to which humans are affecting global warming, can sometimes depend on who is reaching the conclusions.

Degree to how humans are affecting global warming Increase in combustion of fossil fuels (e.g. coal, oil, petroleum, natural gas) increased CO2 concentration (from vehicle usage in farming) Destruction of carbon sinks (e.g deforestation of trees which release CO2 back into the atmosphere when burnt) Fracking (Extraction of shale gas) increases methane emissions as more decaying waste gives off CO2 (also by natural excretion from animals which give off methane as a waste gas) Thawing of permafrost (frozen ground) releases more methane into the atmosphere as temperature increases

Actions to reduce global warming Reduce CO2 concentration Biofuels - produced from plants which was recently living. Replace fossil fuels. Although produces CO2, there is no net increase in CO2 concentration (carbon neutral) Reforestation - Planting of new trees in existing forests that have been depleted. More CO2 is absorbed, so less CO2 is kept in the atmosphere and is used for photosynthesis instead. Building more wind turbines which would produce electricity without increasing the CO2 concentration

In favour of strategies Governments can fund the farming of crops for biofuels (Farmers) Price of biofuels is lower than oil based fuels Sales of wind turbine companies would increase Wind turbines do not increase the CO2 concentration

Against strategies Forests will be cleared to create land for farming of crops for biofuels Using farmland to grow crops for biofuels can lead to food shortages Wind turbines have killed many birds Wind turbines ruin the landscape.

Why scientific conclusions about global warming depend on who is reaching the conclusions Conclusions made are judged on Reliability of data Evidence No direct evidence to show a causal link between variables Consideration of other limiting factors Evidence is past from being used Past evidence is not an indicator of future events Bias Scientists may be biased May be employed by a company with vested interest Conclusions arent objective and are based off an opinion)

21. Describe how evolution (a change in allele frequency) can come about through gene mutation and natural selection.

Evolution - A change in the allele frequency over time Conditions for evolution Variation - Must be differences between the individuals in a population Heredity - Differences between organisms must be heritable Means of selection - Must be a mechanism or pressure that favours some variables for the next generation over others. How genetic variation can arise Gene mutations: Deletion or addition of a nucleotide Deletion or translocation of part of a chromosome Aneuploidy - Loss or gain of a single chromosome Polyploidy - Addition of a whole chromosome Meiosis Independent assortment Crossing over

Natural Selection There is a struggle for existence more offspring are made than survive Selection pressure Condition that favours organisms with alleles that code for advantageous traits

Types of selection: Disruptive - Selection pressure towards both extremes, creating 2 modal values Stabilising - Selection pressure towards centre, this increases the number of individuals at the modal value Directional - Selection pressure moves towards the one extreme moves the mode in this direction Humanity as a selection pressure Use of antibiotics [bacteria that carry allele for resistance will survive and reproduce] Produces a resistant population Artificial selection Humans decide which members of a population will breed Allows desirable alleles to be maintained in the gene pool of a population Used by farmers to produce animals, and plants with a high yield Can lead to inbreeding low genetic diversity This can increase risk of disease

22. Explain how reproductive isolation can lead to speciation. Speciation - The formation of a new species over time Gene pool - Complete range of alleles in a population of a species. Genetic drift - Change in allele frequency over time. This occurs when gene flow between a population has been stopped where it once previously existed Requires 2 populations of the same species to be reproductively isolated Reproductive isolation - Change in allele frequency causes changes in phenotype, therefore separate populations can no longer breed together to produce fertile offspring

Allopatric speciation Populations are geographically isolated Populations are each exposed to different conditions in their environments Become adapted to their environments (by natural selection) giving rise to different phenotypes Mutations and change in allele frequencies Will become reproductively isolated and populations will no longer produce fertile offspring together

Sympatric speciation Occurs in same place (no geographical isolation) Species exist in breeding populations (demes) Demes are reproductively isolated due to changes in the reproductive mechanism Also one population may carry beneficial alleles to exploit and be adapted to a microhabitat Causes of Reproductive isolation: Pre zygotic barriers Habitat - Select diff. habitats, therefore do not meet Temporal - Have different mating or flowering periods Behavioural - Have different mating calls, therefore cannot recognise members of other population as mating partners Mechanical - Anatomical differences in genitalia prevent fertilization Gametic - Female gamete fails to meet male gamete Post zygotic barriers Low hybrid zygote vigour - Zygote fails to develop properly and dies during embryonic development/ offspring has severe abnormalities Hybrid invibility- Offspring fails to thrive and grow properly Hybrid infertility - Offspring appears healthy but infertile

23 Describe the role of the scientific community in validating new evidence (including molecular biology, eg DNA, proteomics) supporting the accepted scientific theory of evolution (scientific journals, the peer review process, scientific conferences).

Anatomical Evidence: Living species: Darwin's Finches and their anatomical differences (beaks) which were suitable for their niche. Fossils: Some show transition between animal groups. Often a missing link is based off of anatomical features. Comparative anatomy: Limbs of living and extinct species show similarities anatomically. Suggests organisms are likely to share a constant ancestor. Artificial selection: Selective breeding (e.g the domestication of animals by humans) Humans provided selection pressures showing animals can undergo dramatic changes.

Molecular evidence: DNA genetic code is universal Respiration and ATP universal molecule for energy storage All have DNA and RNA Proteins in all organisms, formed from the same 20 amino acids All have phospholipid membranes Similar metabolic pathways

Proteomics Study of similarities in protein size and shape Amino acid sequence is coded by the DNA sequence Look at similarities in DNA sequences Look at similarities in amino acid sequences Organisms that have undergone speciation recently will have more similarities Genomics Study of similarities in DNA base sequences in the genes Analysed by DNA hybridisation/profiling/molecular clocks Distantly related species will show less similarities due to the high number of mutations occurring over time

Validating new evidence Scientific journals are used to share theories These can then be validated by peer review for validity Replicating the experiment to test for reliability and validity Scientific questions allow theory to be discussed This retains validity

Reliability - Repeatability; to what extent can the same results be produced again Validity - To what extent have other factors been taken into account and controlled Precision - Results show minimal error Accuracy - Results are close to true value