Biology Unit 4, Topic 5

  • Created by: Emily
  • Created on: 06-06-13 19:45


Photosynthesis involves the reduction of carbon dioxide (CO2) to carbohydrate. These carbohydrates can be used to provide energy in respiration. The hydrogen for this process comes from the splitting of water by light, the waste oxygen being release into the atmosphere. 

The overall equation for photosynthesis is:

6CO2 + 6H2O ---light & chlorophyll---> C6H12O6 + 6O2

The splitting of water is called photolysis. The energy for this step is first trapped by a pigment molecule called chlorophyll. 

There overall process is achieved in two linked stages called the light-dependent reactions and the light-independent reactions. 

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The Light-Dependent Reactions

  • In this process, a pair of electrons from chlorophyll is boosted to a higher energy level by the light energy it has trapped. Here they are accepted by an electron acceptor and then passed along a chain of carriers.
  • Energy released is used to convert ADP and inorganic phosphate (Pi) into ATP. This process is called photophosphorylation (the light-driven addition to phosphate).
  • The electrons then enter another chlorophyll molecule. 
  • The electrons eventually pass to NADP with the hydrogen from water to form reduced NADP. 
  • The ATP and reduced NADP are then used in the light-independent reactions to make carbohydrate from carbon dioxide.
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The Light-Independent Reactions

The light-dependent reactions make ATP & reduced NADP which are then used in the light-independent reactions (Calvin Cycle).

The reduced NADP provides reducing power (electrons or hydrogen) and the ATP provides the energy for the process of making carbon dioxide into carbohydrate.

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The Calvin Cycle

  • Carbon dioxide combines with a 5-carbon compound called RuBP. This reaction is catalysed by the enxyme RuBISCO.
  • The 6-carbon compound formed is unstable and immediately breaks down into two 3-carbon molecules, GP.
  • This 3-carbon compound is reduce to form a 3-carbon sugar phosphate called GALP. The hydrogen for the reduction comes from the reduced NADP from the light-dependent reactions. ATP from the light-dependent reaction provides the engery required for the reaction.
  • Two out of every 13 GALPs formed are involved in the creation of a 6-carbon sugar (hexose) which can be converted to other organic compounds e.g. amino acids or lipids.
  • Ten out of every 12 GALPs are involved in the recreation of RuBP. The 10 GALP molecules rearrage to form six 5-carbon compounds; then phosphorylation using ATP forms RuBP.
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Adenosine triphosphate (ATP) provides energy for chemical reactions in the cell. When energy is needed, phosphate is removed from the ATP to give ADP and a phosphate. The energy is release when the phosphate forms bonds with water. In the photosynthesis light-dependent reactions, ATP is made using energy from light.

ATP -------> ADP + Pi + Energy

In photosynthesis, the ATP made is used as a source of energy in the light-independent reactions. ATP is also used widely in organisms as a way of transferring energy. It is an intermediate between energy-producing reactions & those that need energy.

Some of the glucose made in the Calvin cycle is used by the plant in respiration. The rest is used to sythesise all the molecules on which the plant relies, for example simple sugars, polysaccharides, amino acids, lipids & nucleic acids. 

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Where does Photosynthesis happen?

In all eukaryotic cells there are mebrane-bound structures called organelles. These are the sites of specialised processes within the cell. For photosynthesis, plant cells have a structure called the chloroplast

  • Thylakoid membranes - a system of interconnected flattened fluid-filled sacs. Proteins, including photosythetic pigments & electrons carriers, are embedded in the membranes & are involved in the light-dependent reactions.
  • DNA loop - chloroplasts contain genes for some of their proteins.
  • Stroma - the fluid surrounding the thylakoid membranes. Contains all the enzymes needed to carry out the light-independent reactions of photosynthesis.
  • Thylakoid space - fluid within the thylakoid membrane sacs contains enzymes for photolysis.
  • Granum - a stack of thylakoids joined to one another - grana (plural).
  • Smooth inner membrane - contains many transporter molecules. These are membrane proteins which regulate the passage of substances in & out of the chloroplast. These substances include sugars & proteins synthesised in the cytoplasm of the cell but used with the chloroplast.
  • Smooth outer membrane - which is freely permeable to molecules such as CO2 & H2O
  • Starch grain - stores the product of photosynthesis
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Energy transfer, abundance & distribution

Plants make glucose in photosynthesis. This can be turned into other molecules including starch, cellulose, proteins & fats. This biomass is food for both humans & every other living thing on Earth, including the plants themselves.

The rate at which energy is incorporated into organic molecules in the plants in photosynthesis is called gross primary productivity (GPP). Plants use some of the organic molecules in respiration. If we find out the figure of GPP & take away the amount of energy used in respiration (R), what is left is the rate at which energy is transferred into new plant biomass that can be eaten by herbivores or decomposers. This is called net primary productivity (NPP). All these variabes are measured in energy units (kilojoules) per square metre per year (kJm-2 year-1) fixed in photosynthesis or used in respiration.

The relationship between GPP, NPP & R is:


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Energy Transfer

Herbivores eat plants. The energy in the food is transferred from the primary producers (plants) to the herbivores. They use must of the energy in respiration for movement in the body. Some energy is lost as heat to the environment. The rest is available for other animals or decomposers. 

Energy trapped (GPP) - Energy plants use in repiration (R) = net primary productivity (NPP)

The transfer efficiency from producers to primary consumers is the amount transferred to the primary consumers, divided by the amount potentially available to them. 

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Distribution & Abundance

In any habitat a species occupies a specific niche determined by environmental conditions (biotic and abiotic factors) and the way that the species uses the habitat (food, shelter, sites, feeding times etc.). The distribution (where they are) and abundance (how many) are determined by these conditions. Changes in these conditions can therefore lead to changes in distribution and abundance. 

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Primary succession happens when an area which is devoid of life is first colonised by species (usually lichen and algae on bare rock) that can cope in the harsh conditions. These are called pioneer species. They alter the environment in a way that makes it an unsuitable home for them, but suitable for new species to establish. The new species often replace the existing species. A similar process occurs time and again, through stages known as seres, until a stable community is reached.

In stable woodland, for example, trees die but new ones of the same species grow to fill the gap. This is a climax community. If the succession starts with living things already present, for example if grazing stopped in a meadow, which then became woodland, this is called secondary succession

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Investigating numbers & distribution

Investigating where organisms live (distribution) and how many there are (abundance) depends on what kind of habitat we are in and what we want to find out. If there appears to be a change across the area, a transect is the preferred method. If two areas appeared different and we wanted to compare them, we could take random samples within each area. In both cases we would use a quadrat to estimate abundance. 

In either case, the usual methods to estimate abudance would be:

  • Either count the individuals in a quadrat - this is not easily done with many plants, such as grasses, but quite possible with organisms such as limpets. 
  • Or find the precentage cover of each species - this is the most common method with plants. These estimates are best made using a quadrat that is divided up into smaller squares & counting the number of squares/part of squares occupied by each species in turn. If there are 100 squares in the quadrat, then the number of squares/part of squares covered make up the percentage cover for that plant.
  • A different method involves the use of a point quadrat, in which pins are lowered systematically on the vegetation, any 'hits' on the pins are recorded. % cover = hits divided by hits & misses x 100.
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Measuring Factors

  • Solar energy input - use a light metre
  • Climate - information about rainfall & temperature can be ovtained from published sources
  • Topography - topographical surveys measure the shape of the land. Surveryors' levelling equipment can be used - the simplest method being to use ranging poles & clinometers.
  • Oxygen availability - use an oxygen probe
  • pH - use a pH probe or soil pH kit
  • Minerals - gardener's test kits can test the levels of important nutrients such as nitrate, phosphate & potassium (NPK).
  • Water - soil sample can be weighed, dried slowly in an oven and reweighed to give the mass of water.
  • Organic matter - the dry soil sample can be weighed, burnt in a crucible & reweighed. Any organic matter is burnt off, which account for any difference in mass.
  • Soil texture - soil texture charts can be used to assess if the soil is mainly clay, silt or sand.
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The theory of evolution is about how & why organisms have changed over time. What actually changes is allele frequency (the relative frequency of a particular allele in a population). New alleles arise from random changes in the DNA which makes up genes (gene mutations) and create variation within the population. Once a gene mutation has appeared it is acted upon by the selection pressures in the environment. 

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In order for new species to form, part of an existing population must become reproductively isolated from another part. This usually happens when a barrier comes between two or more parts of an existing population. Over time, natural selection may cause the different parts of the population to change to such ecten that they can no longer interbreed to produce fertile offspring and this make them two or more different species. 

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Types of Barriers

Prezygotic reproductive barriers

  • Habitat isolation - population occupy different habitats in the same area so do not meet to breed.
  • Temporal isolation - species exist in the same area but are active for reproduction at different times.
  • Mechanical isolation - the reproductive organs no longer fit together.
  • Behavioural isolation - populations do not respond to each other's reproductive displays.
  • Gametic isolation - male & female gametes from 2 populations are simply incompatible with each other.

Postzygotic reproductive barriers

  • Hybrid sterility - healthy individuals produced from the mating of 2 different species cannot themselves reproduce (e.g. the mule).
  • Hyrbrid inviability - individuals produced from the mating of 2 different speices are not healthy & do not survive.
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New Evidence

Darwin's theory was very debatable. There are now new types of evidence supporting the theory available to us:

  • The DNA molecule is the same in all organisms. This supports Darwin's idea of descent from a common ancestor.
  • DNA & proteins contrain a record of genetic changes that have occurred by random mutations over time, indicating gradual change withing & between species. By studying DNA & proteins these changes can be identified. Comparting the DNA or amino acid sequences in different species can show how closely related species are in evolutionary terms. The more similar the sequence, the more closely related the species.
  • Assesing the speed of mutation in DNA has shown that species have evolved over vast periods of time, as Darwin thought.
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Validating Evidence

Any new evidence must be carefully studies before it can be accpeepted. The scientific process has 3 key aspects which try to ensure reliability & validity:

  • Dedicated scientific journals
  • Peer Review
  • Scientific conferences

There are thousands of scientific journals published worldwide. Any research carried out must be published in at least 1 of these so that it can be read by other scientists. However, before it even gets to this stage it has to undergo a process called peer review. The editor of the journal sends a potential paper to 2 or 3 other scientists in the same area of work. They generally ask

  • Is the paper valid? (are the conclusions based on good methods & is the data reliable?)
  • Is the paper scientific? (it must make a useful addition to the existing body of scientific knowledge)
  • Is the paper original? (or has someone already done the same work?

Only if the other scientists agree that the paper is all these things can it be published.

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Greenhouse gases & the carbon cycle

There are a number of key questions to be asked:

  • Are CO2 levels rising and is there global warming?
  • Does one cause the other?
  • How bad will it get and can we do anything to combat it?

To answer these questions, we need to look at evidence from many different sources.

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Evidence for global warming

  • Temperature records - long-term data sets allow changes in temperature to be analysed, e.g. the Central England Temperature series has records from 1659 to the present.
  • Tree rings - studying the size of tree rings is called denrochronology. If the climate is warmer & wetter then the rings are wider. We can look at tree ring widths over 3000 years into the past can can tell a lot about the climate from them.
  • Pollen data - pollen grains are preserved in peat bogs. By sampling at different levels in the peat we are sampling at different ages. Analysis of the pollen can tell us which plants were growing and so what the climate was like when the peat was formed.
  • Ice cores - air trapped in ice when it was formed thousands of years ago can be analysed. This give us information about temperatures & CO2 levels in the past.
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Greenhouse Effect

Cabon dioxide in the atmosphere is known as a greenhouse gas. It allows radiation to reach the Earth from the Sun. Some of this energy is trapped by CO2 and the Earth warms up. This is the greenhouse effect. Other gases also have this effect e.g. methane.

  • Most ultraviolent is absorbed by the ozone int he stratosphere
  • Some visible radiation is reflected by the Earth
  • Some is reflected by the clouds
  • Most solar radiation is absorbed by the Earth's surface, which warms up
  • Some infared is absorbed by greenhouse gases, warming up with troposphere
  • Some infared emitted by the Earth's surface escapes and cools down the Earth

The data supports the theory of global warming being caused by humans, due largely to CO2 and methane emissions.

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Computer Modelling

Any attempt to predict climate change in the future must rely on very complex computer models to extrapolate from what we know to what might happen.

These models get better all the tme but they are limited by lack of computing power, sufficient data and knowledge of how the climate functions.

Some factors such as carbon dioxide emissions or changes in ice cover are very hard to predict. 

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What can be done?

The Carbon Cycle

It is clear that there are a number of inputs & outputs to and from the atmospheric reservoir of CO2. Until recently, the two have largely been in balance but now it is clear that there is extra CO2 being added to the atmosphere by human activity. Things we can do:

  • Plants take in CO2 in photosynthesis, and trees store a lot of CO2 as they gain size. Deforestation is thought to be an important cause of CO2 increase in the air. Therefore large-scale planting of new trees could reduce the amount of CO2 in the atmosphere. Reforestation will increase the removal of carbon dioxied from the atmosphere due to an increase in photosynthesis. 
  • Another way of reducing CO2 levels would be to grow plants to use a fuel. They would only release the CO2 they had just taken in and so would be carbon neutral. However, chopping down rainforest to grow palms for oil releases more CO2 than it takes in, and using corn to make ethanol for biofuel deprives people of food. 
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Impacts of Global Warming

Global warming will impact on the climate in many ways. In Britain, a rise in temperaure might mean warmer, wetter winters. Rainfall patterns are also likely to be effected. This might mean an increase in flooding in some areas. In other areas the risk might be drought. Finally the seasonal cycle may change so that seasons are different in length & inesnsity. All of these will affect plants & animals in 3 main ways:

  • Changes in species distribution - as the average temperature rises, species in the south of the UK may withdraw northward & those restricted to places further north may extend southward. Also, species which cannot live in these areas now may move in (alien species) & out-compete native species, making them extinct in the area.
  • Changes to development - in many reptiles, the temperature affects the s*x of young that hatch from eggs, so warming could cause a change in s*x ratios in these species.
  • Changes to life cycles - organisms where temperature is an important trigger for development may well have their life cycles disrupted. Insects may get through their life cycle more quickly & be ready to feed before the plants they feed on are mature.

Temperature affects enzymes & therefore whole organisms - plants, animals & microorganisms. Organisms may grow faster if temperatures rise a few degrees. However, if the temperature rises too high their enzymes will denature & all reactions will stop.

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Brine Shrimp Practical

We can investigate the effect of temperature on hatching rates in small invertebrates called brine shrimps. In this practical we want to vary temperature (independent variable) and see how it affects the number of shrimps hatched (dependent variable).

There are other variables which might affect the rate such as salinity, pH & light level. It is important to keep these controlled or monitored during the experiment, both to make the data valid, and to care for the experimental animals.

It is also possible to study the effect of temperature on seedling growth rates. In both experiments datalogging can be used to monitor the temperature and ensure reliable results. 

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Who Decides?

There is little doubt that global warming is happening, but there are still big questions over what is causing it ad what we should do about it.

It is quite normal for scientists to disgree but this topic is also a matter for public debate. Non-scientists may not understand the uncertainty and naturall want a clear answer. The peopel who will give them this are often not the scientists but politicians, economists adn other policy makers. Quickly the debate becomes politicised and then the usual impassionate methodology of science becomes sidelined.

It soon become clear that data are being interpreted with various hidden agenda and then this becomes the news rather than the science itself. So, scientists are accused of being funded by oil companies if they argue against the established poltical view, or politicised if they argue for it.

What conclusions people reach are often coloured by who funded the research they are doing, and pressures of economics and politics.

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thank you soo much! very good!




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