Monday, 29 December 2014

Geographic separation of populations of a species can result in the accumulation of difference in the gene pools. The importance of geographic isolation in the formation of new species

If you split a population in two and put one of them in different conditions with no interbreeding, then over a long time the two groups would have such different gene pools that they would no longer be able to breed to create fertile offspring.

This is because there would be different mutations and selection pressures and so different alleles would be selected due to differential reproductive success causing a change in allele frequency.

This happens naturally in nature as populations become geographically separated, meaning there is something in the way of groups of a species breeding with each other e.g. a river.

Differential reproductive success and its effect on the allele frequency within a gene pool. Directional and stabilising selection. Candidates should be able to • use both specific examples and unfamiliar information to explain how selection produces changes within a species • interpret data relating to the effect of selection in producing change within populations

A species will be made mostly up of individuals with alleles that mean they reproduce more (as they have more children so there are more of them).

This doesn't necessarily mean alleles that make them more fertile, it could be things that make them stronger to fight off competition, it could be things that make them grow quicker to have a longer reproductive lifespan or it could be things that make them less likely to die (and therefore not be able to have children).

Over time alleles that for filled these criteria may no longer due to changes in the environment: for example a flower that is adapted to hot conditions will live longer in a hot climate and therefore have more offspring (the alleles for surviving in hot conditions will be plentiful in the gene pool), if the climate then becomes cooler, this flower will no longer have an advantage over the other flowers in terms of life span it will therefore produce an average amount of offspring (and the alleles for surviving in hot conditions will decrease in the gene pool).

In this example a hot climate caused a selection pressure towards plants that could with stand warm conditions and changed the gene pool, this is called a directional change: where certain characteristics are favoured by a change in environment.

Red line = new curve

We then saw that when this pressure was removed, and the environment was stable the extreme allele of heat resistance was selected against and alleles closest to the mean are favoured. This is called stabilising change.

The classic example of directional change is that during the industrial revolution more soot was on trees which made them darker, so the alleles in the moth population switched from which to black for camouflage. For stabilising selection an example is the size of babies heads, because the size of the pelvis is not changing it is a disadvantage to have a big head as it will not fit through increasing the chance of death and it is not good have a small head as infant mortality is higher among small babies, therefore the extremes of head size are selected against and the most favoured alleles are those closest to the mean.

Species exist as one or more populations. The concepts of gene pool and allele frequency. The Hardy-Weinberg principle. The conditions under which the principle applies. Candidates should be able to calculate allele, genotype and phenotype frequencies from appropriate data and from the Hardy-Weinberg equation, p2 + 2pq + q2 = 1 where p is the frequency of the dominant allele and q is the frequency of the recessive allele. Candidates should understand that the Hardy-Weinberg principle provides a mathematical model which predicts that allele frequencies will not change from generation to generation.

A gene pool is all the genes that exist in a population. So say we take a population of rabbits and they are all albino then we know that the genes in this pool are albino. Say we take a population of rabbits and there are some of each colour then we know the gene pool has grey, chinchilla, himalayan and albino in it.

In this second population of rabbits there will be higher numbers of some colours than others. The amount of times an allele crops up is known as allele frequency.

The Hardy-Weinberg principle is an equation that allows us to work out the frequency of alleles in a population.

It states that the frequency of alleles will stay constant from one generation to the next provided that: there is genetic isolation; the population is large; mating is random; there are no mutations; there's no natural selection; there's no migration.

Here is how it works:

We use the short hand p to represent the dominant allele and q to represent the recessive allele.

We know that if you added up all of the dominant alleles and all of the recessive alleles the total would be all the alleles (100%) so:

p+q= 1.0

We also know that if you took all the possible genotype and added them up you would get all the alleles:
So DD + Dd + dD + dd= 100% or

p2 + 2pq + q2= 1.0

From these two equations, if given the information on one phenotype, you are able to work out different things about a population. Here is  a worked example:

A sample of a population shows that 36% of a population is homozygous recessive (aa). Find the frequency of the dominant phenotype.

So the first thing you want to do is work out what they are asking you for, and in this case it would be any genotype with the dominant gene in so Aa and aa, so 2pq plus p2. And what have they given you: aa which is  q2. I like to then write out a list of what I have and what I need:

q2= 0.36
p2 + 2pq=

As stated earlier we know that p+q= 1.0 (or 100%) so we know that 1.0-q will give us p:

Square root of q2= sqrt 0.36 = 0.6
p= 1.0-0.6= 0.4

So we now have:

q= 0.6
p= 0.4
q2= 0.36
p2 + 2pq=

So to work out p2 we square p= 0.16
and to work out 2pq we do 2 x p x q = 0.48

and to work out the answer we do 0.16 + 0.48= 0.64

The genotype is the genetic constitution of an organism. The phenotype is the expression of this genetic constitution and its interaction with the environment. Alleles are one or more alternative versions of the same gene. The alleles at a specific locus may be either homozygous or heterozygous. Alleles may be dominant, recessive or codominant. There may be multiple alleles of a single gene. Candidates should be able to use fully labelled genetic diagrams to predict the results of • monohybrid crosses involving dominant, recessive and codominant alleles • crosses involving multiple alleles and sex-linked characteristics.

An allele is a form of a gene (e.g. brown hair).

A genotype is all the alleles that an organism possesses in its genetic code.

A phenotype is the allele that gets expressed in proteins. Phenotype also accounts for environmental factors, so if you die your hair.

A locus is an area of DNA which codes for a protein, so where a gene is stored.

In an organism there are two sets chromosomes, one from each parent, and on a pair of chromosomes at the same locus there will be two alleles for the same characteristic; you could either have two of the same allele (homozygous), or you could have two different alleles (heterozygous).

In general only one of the two alleles will be expressed, so how does the body decide which one? Well, some alleles are dominant and some are recessive, this means that a dominant characteristic will always be produced if it is present, and a recessive one only gets produced when both the alleles are recessive.

On the last pair of chromosomes (23 in humans) the two chromosomes may not be identical, one may be shorter than the other and so not have a matching gene. This short version of the chromosome is called the Y chromosome and it is what makes humans male. So a female is XX and a male is XY. Having only one version of a gene is dangerous because it means that you are more likely to have only recessive genes, and often diseases are caused by recessive alleles, for example colour blindness, this means men are more susceptible to certain problems. Women can still get these problems, but it is less likely as they would have to get 2/2 recessive genes.

In some genes there is co-dominance, this means that some alleles will both be expressed if they are both present. For example if a cow has two white alleles it will be white, and if it has two black it will be black, but if it has one of each they will both work so it will come out with bits of black and white.

In general there are only two alleles for a gene, one dominant and one recessive, but in some cases there are many more alleles. In this case, to decide which one gets produced there is a hierarchy of alleles. For example rabbit fur is determined by four alleles:

The table shows the alleles in order of dominance, with grey being dominant over everything and albino being recessive to everything. So if we have a chinchilla allele with a grey allele we will get a grey rabbit; but if we have a chinchilla allele with any other allele, chinchilla, himalayan or albino, we will get a chinchilla rabbit.

Succession from pioneer species to climax community. At each stage in succession, certain species may be recognised which change the environment so that it becomes more suitable for other species. The changes in the abiotic environment result in a less hostile environment and changing diversity. Conservation of habitats frequently involves management of succession. Candidates should be able to • use their knowledge and understanding to present scientific arguments and ideas relating to the conservation of species and habitats • evaluate evidence and data concerning issues relating to the conservation of species and habitats and consider conflicting evidence • explain how conservation relies on science to inform decision-making.

Succession is the idea of the sorts of plants and animals in a habitat changing over time. There are two types: primary succession occurs when there is a totally bare piece of land, like a rock or somewhere that has been wiped out by a volcanic eruption.

Pioneer species are the first living things to grow on the land, they are renowned for being able to withstand tough and extreme conditions that other plants cannot live in. Often they get there because they have spores or windblown seeds which are easily transported from other communities. Once there they reproduce rapidly, as this is often a feature of pioneer species. The plants will photosynthesise to produce energy, they may also produce nitrogen by bacteria on their root nodules as there will be little existing nutrient in the soil.

When the plants from the pioneer species die and decompose, they leave deposits of nutrients; the beginnings of soil. This soil is rich in humus (organic matter) which other plants need to survive, this means that other species can begin to grow. These plants then decompose in turn increasing the humus even further, and the depth of soil, so new species can move in that are less hardy and have bigger roots. This cycle continues: often the original species are out competed by newer ones; at some point when there are enough plants animals will join the system.

Secondary succession is when a minor disturbance kills off plants, but leaves soil and possibly seeds behind. Here the same process of succession will happen, but as the conditions are less hospitable it does not need a pioneer species to start it off.

The further into succession, the higher the biodiversity as conditions become less hostile and are more friendly to live in for more organisms. Not only is this caused by an improvement in soil, but things like also a decrease in wind, changes in soil acidity and a greater variety of habitats.

We have the idea of a climax community which is the sorts of plants and animals that will grow in an area once it has reached equilibrium. For example, in England, due to the climate, most areas stop changing the species when there is deciduous oak woodland.

Because different plants and animals are suited to different stages of succession, if conservationists are trying to increase the population of a plant or animal, they will control succession to be at the stage that that organism is successful at.

Sunday, 28 December 2014

The environmental issues arising from the use of fertilisers. Leaching and eutrophication. Candidates should be able to analyse, interpret and evaluate data relating to eutrophication.

Nitrogen is circulated between existence in the atmosphere, in the soil, and in living things. The diagram shows how nitrogen is passed from one form to another.

In plants, animals and decomposers nitrogen exists as ammonium containing molecules like proteins and nucleic acids.

In farming this natural cycle is disrupted because dead matter is removed from the area (as is waste). This means that nitrogen in the soil is not replaced and so fertilizers must be used to replenish levels so that plants can grow there.

Natural fertilisers consist of waste and or dead matter. Artificial fertilisers are made from nitrogen extracted from rocks or made in the harbour process.

Eutrophication happens when water leeches nitrogen from soil and takes it into a water system: here the nitrogen helps algae to grow causing a bloom (large layer of algae); this blocks light for other organisms, like fish, and uses up their oxygen, causing them to die; decomposers increase as they feed on the dead, using up even more oxygen; oxygen is so low that no other organisms can survive.

Nitrogen can leech into supplies of drinking water too.

The role of microorganisms in the carbon and nitrogen cycles in sufficient detail to illustrate the processes of saprobiotic nutrition, ammonification, nitrification, nitrogen fixation and denitrification. (The names of individual species are not required.)

Saprobiotic micro-organisms are ones which get their nutrition from dead matter. They decompose plants and animals, releasing carbon and nitrogen back into the air and soil, helping to make the movement of these molecules a continuous cycle.

Ammonification- creating ammonium from molecules that contain it; done by saprobiotic micro-organisms

Nitrification- turning ammonium into nitrate; this is done by some bacteria to create energy

Nitrogen fixing- turning nitrogen in the air into ammonium; done by free living bacteria to create amino acids for themselves; done by mutualistic bacteria to create amino acids for plants in return for carbohydrates

Denitrification- carried out by bacteria for energy

Nitrifying-bacteria are aerobic and denitrifying-bacteria are anaerobic, so if soil is water logged there will be a decline in nitrification and an increase in denitrification.

The importance of respiration, photosynthesis and human activity in giving rise to short-term fluctuation and long-term change in global carbon dioxide concentration. The roles of carbon dioxide and methane in enhancing the greenhouse effect and bringing about global warming. Candidates should be able to analyse, interpret and evaluate data relating to evidence of global warming and its effects on • the yield of crop plants • the life-cycles and numbers of insect pests • the distribution and numbers of wild animals and plants.

Carbon goes round in a cycle, below is a diagram to show this. The three grey lines, from plants, animals and decomposers, show carbon being put back into the atmosphere by respiration.

Atmospheric levels of carbon dioxide can be changed short term or long term.

A short term change could be brought about by the balance of photosynthesis and respiration: there is more photosynthesis in the day-light which takes CO2 out of the atmosphere and more respiration at night which gives CO2 into the atmosphere.

A long term change may be brought about by a decrease in plants, as they carry out photosynthesis, or a release of carbon from a store. These are both things that humans cause to happen in deforestation and the combustion of wood and fossil fuels.

Light is radiated to the earth by the sun, it is then reflected back off the earth as heat. Gasses in the atmosphere such as CO2 and methane trap heat, so when it is reflected back off the earth it is not lost, but kept and warms our globe. A rise in greenhouse gasses (ones that stop the heat escaping) causes a rise in the temperature of the earth which is global warming.

The potential effects of global warming are wide spread:

  • Certain plants cannot function at high temperatures
  • Land may be flooded, leaching nitrogen and increasing denitrifying bacteria
  • More energy for reactions (more respiration at night uses up energy stores and decreases yield)

Life cycle

  • Change in seasons may disrupt breeding or metamorphosis
  • Change in heat may mean some plants or animals miss cues that or based on heat


  • Warmer temperatures higher up mean that cold loving things are forced to migrate northwards
  • More weather extremes and the heat change will mean new selection pressures so different species or characteristics are favoured

Saturday, 27 December 2014

Comparison of natural ecosystems and those based on modern intensive farming in terms of energy input and productivity. Net productivity as defined by the expression Net productivity = Gross productivity – Respiratory loss The ways in which productivity is affected by farming practices that increase the efficiency of energy conversion. These include • the use of natural and artificial fertilisers • the use of chemical pesticides, biological agents and integrated systems in controlling pests on agricultural crops • intensive rearing of domestic livestock. Candidates should be able to • apply their understanding of biological principles to present scientific arguments that explain how these and other farming practices affect productivity • evaluate economic and environmental issues involved with farming practices that increase productivity • consider ethical issues arising from enhancement of productivity

In natural ecosystems there is a relatively closed system in terms of energy input, nutrients and energy go around in a cycle from producers to consumers to decomposers with the main input being sunlight.

In modern day farming energy is introduced to a system via feeding, heat and artificial light; this increase in input makes for an increase in out put, a higher yield.

Productivity is the amount of chemical energy that plants make by photosynthesis. The net is calculated by the amount of energy produced from photosynthesis take away the amount that is used by the plant during respiration.

Net productivity= gross production - respiratory loss

In modern day farming farmers use any means possible to increase their yield, and therefore increase their profit.

Natural fertilisers include manure and animal bone; things that naturally contain nitrogen. Artificial fertilizers contain nitrogen made by the harbour process and extracted from rocks.

Pesticides are chemicals that are spread on crops to kill pests (things that are eating or damaging crops). Biological control is the introduction of an organism that will eat a pest. An integrated system is a series of techniques used to try and keep pest damage to a minimum, without disturbing the biodiversity of an area e.g. choosing areas with few pests, encouraging natural predators to be around, removing but not killing pests.

Eutrophication happens when water leeches nitrogen from soil and takes it into a water system: here the nitrogen helps algae to grow causing a bloom (large layer of algae); this blocks light for other organisms, like fish, and uses up their oxygen, causing them to die; decomposers increase as they feed on the dead, using up even more oxygen; oxygen is so low that no other organisms can survive.

Intensive farming also happens with livestock.

1 Slaughtered when still growing/before maturity/while young
 so more energy transferred to biomass/tissue/production;
2 Fed on concentrate /controlled diet /controlled
 conditions/so higher proportion of (digested) food
 absorbed/lower proportion lost in faeces / valid reason for
3 Movement restricted so less respiratory loss / less energy
4 Kept inside/heating/shelter / confined so less heat loss / no
5 Genetically selected for high productivity;

Photosynthesis is the main route by which energy enters an ecosystem. Energy is transferred through the trophic levels in food chains and food webs and is dissipated. Quantitative consideration of the efficiency of energy transfer between trophic levels. Pyramids of numbers, biomass and energy and their relationship to their corresponding food chains and webs.

Ultimately, energy comes from the sun. So how does energy get into the food chain? from things than convert sunlight into stored chemical energy i.e. producers (things that carry out photosynthesis).

An animal will eat a plant to gain the energy, this animals is the primary consumer (first thing to eat) in a food chain. Some of the plant may not get eaten and some may not get digested meaning that the energy does not transfer from the plant to the animal.

Of the energy that is transferred to the animal some will be stored, but some will get used up for carrying out the processes of living (movement, homoeostasis*). This means that when a second animal eats this primary consumer it will only get a very small amount of energy from the original plant.

*a lot of energy is used up by warm blooded creatures (mammals and birds) because they use it to maintain their body temperature.

1 Some light energy fails to strike/is reflected/not of
 appropriate wavelength;
2 Efficiency of photosynthesis in plants is low/approximately
 2% efficient;
3 Respiratory loss / excretion / faeces / not eaten;
4 Loss as heat;
5 Efficiency of transfer to consumers greater than transfer to
 producers/approximately 10%;
6 Efficiency lower in older animals/herbivores/ primary
 consumers/warm blooded animals/homoiotherms;
7 Carnivores use more of their food than herbivores;

We can see how efficient an energy transfer is, or how much energy actually gets passed on, by looking at how much energy an animal took in and how much it gave out; this shows us how much energy is lost at that trophic level. So if you are given a food chain that asks you to calculate the efficiency of a transfer between a worm and a bird of prey, and the worm has 6500 (kjm-2year-1) of energy available and the bird has 1500 (kjm-2year-1) of energy avalible then:

Efficiency= energy after/energy before * 100
= 1500/6500 * 100
= 0.23 * 100
= 23%

Because energy is lost between levels, you might assume that there would always be fewer animals as you went up trophic levels as there is less energy. This would be the case in the food chain of algae, fish, bird:

Pyramid of number
However there are examples where this is not the case. If we look at a food chain surrounding a tree, often the organisms that feed off the tree are very small and the tree is very big, so one tree can feed many organisms:

Pyramid of number
A way to make sense of this is to use a pyramid of biomass. This is basically like saying the weight of the organisms on a level (this does not include the weight of water because it disrupts the figures; so dry mass). For this example if we weighed the tree, all the insects and all the birds, we would end up with something like this:

Pyramid of biomass
Pyramids of biomass are a much more reliable way of representing food chains, but in practice it is difficult to collect accurate data on the weight and number of organisms due to factors like seasonal change and movement.

Another problem with them is that there is a big difference between the energy stored in certain molecules; for example you may have a very heavy organism packed with carbohydrate that would have less energy than a lighter organism covered in fat. A way to get round this problem is to use a pyramid of energy which displays the amount of energy at each level:

Pyramid of energy

Glycolysis followed by the production of ethanol or lactate and the regeneration of NAD in anaerobic respiration.

The first stage of respiration is the same in aerobic and anaerobic respiration; glycolysis. This is because it does not involve oxygen so is not hindered if it is not present.

Two ATP are used to add phosphate groups to glucose, creating phosphorolated glucose. This splits into two molecules of triosephosphate which has phosphate removed by ADP and is reduced byv NAD to make pyruvate.

By doing these things the cell has a net gain of 2ATP and so has respired, but with a much lower energy yield than aerobic respiration.

Usually at this stage NADH would go on to the Krebs cycle, lose its hydrogen, and become NAD again, ready to take part in some more glycolysis. However there is no oxygen, so there is no Krebs cycle, this would mean that NAD was not avalible because it was all NADH.

To solve this problem the pyruvate takes the hydrogen from the NADH making it NAD again. Pyruvate and hydrogen can make one of two things: ethanol + carbon dioxide or lactic acid.

In some plants and in yeast ethanol and CO2 are produced, and in animals it's lactate.

Monday, 22 December 2014

Aerobic respiration in such detail as to show that • glycolysis takes place in the cytoplasm and involves the oxidation of glucose to pyruvate with a net gain of ATP and reduced NAD • pyruvate combines with coenzyme A in the link reaction to produce acetylcoenzyme A • in a series of oxidation-reduction reactions the Krebs cycle generates reduced coenzymes and ATP by substrate-level phosphorylation, and carbon dioxide is lost • acetylcoenzyme A is effectively a two carbon molecule that combines with a four carbon molecule to produce a six carbon molecule which enters the Krebs cycle • synthesis of ATP by oxidative phosphorylation is associated with the transfer of electrons down the electron transport chain and passage of protons across mitochondrial membranes.

The first stage of respiration is glycolysis, it happens in the cytoplasm of every cell.

Glucose is phosphorolated (has phosphate groups added) using ATP. This is then split in two to make two triosephosphates. ADP is then used to remove the phosphate and four ATP are created (two from each triose phosphate molecule). NAD is used to remove hydrogen resulting in reduced NAD (NADH). The result of this is two pyruvate molecules.

So we have a net gain of two pyruvate molecules, two ATP and two NADH. These molecules move into the mitachondria.

The pyruvate is then reduced, has carbon removed and has a molecule called coenzyme A added: this makes it into Acetyl CoA.

This process is known as the link reaction as it turns pyruvate into Acetyl CoA ready for the Krebs cycle.

In the Krebs cycle, Actyle CoA joins with a four carbon compound resulting in a six carbon compound, this is then reduced by NAD and FAD, has carbon removed and looses phosphate to ADP.

The result of this is NADH, FADH, two CO2 and one ATP.

NADH and FAD are carrying protons and electrons (because that's what hydrogen is made up of). At the inner membrane of mitachondria there are proteins which take the electrons from NADH and FADH and pass them along; this is known as an electron transport chain. At the end of the electron transport chain the electrons join with hydrogen and oxygen to create water (this keeps the concentration of hydrogen in the matrix low).

As the electrons are being passed along the etc energy is released and this is used to actively transport protons/hydrogens across the inner membrane into the inter-membrane space. Once in this space the protons/hydrogens want to move back over because they are in a higher concentration there than in the matrix; they diffuse back through an enzyme called ATP synthase and as they do so it gives the enzyme the energy to join ADP and Pi to create ATP.

Friday, 19 December 2014

The principle of limiting factors as applied to the effects of temperature, carbon dioxide concentration and light intensity on the rate of photosynthesis.

There are certain things that are needed for photosynthesis to take place. The availability of these things affects the rate of reaction.

If there is a lack of something that is needed then the rate of reaction will decrease, making it a limiting factor.

Temperature can be a limiting factor because heat energy increases kinetic energy and therefore there are more collisions and so more enzyme-substrate complexes formed.

Temperature directly correlates to rate of photosynthesis until it gets over a heat where it will denature enzymes; then the rate will decrease as there are fewer enzymes to aid the reactions.

Carbon dioxide is a chemical used so the more of it there is the more reactions can be done and visa versa.

Light intensity has an effect because the protons from light are what power the light-dependent reaction, so if there is not enough light the process will happen less frequently.

The light-independent reaction in such detail as to show that • carbon dioxide is accepted by ribulose bisphosphate (RuBP) to form two molecules of glycerate 3-phosphate (GP) • ATP and reduced NADP are required for the reduction of GP to triose phosphate • RuBP is regenerated in the Calvin cycle • Triose phosphate is converted to useful organic substances.

In the stroma of a chloroplast the light-independent stage of photosynthesis happens. It involves taking up carbon to make glucose using the products from the light-dependent stage.

The molecule RuBP (ribulose biphosphate) is made up of five carbons, a molecule of carbon from CO2 is added to make a six carbon compound. This is very unstable and quickly breaks down into two bits of GP (glycerate 3-phosphate) each with three carbons.

GP is then reduced by NADPH, which gives over its H to become NADP, and restructured by ATP, giving energy as it breaks bonds. The molecule made from this is triose phosphate and because there were two GP we have two triose phosphate molecules too.

One carbon is removed, and this carbon is used to make glucose. There are 6 carbons in a glucose so it is made every sixth time the process is repeated.

The remaining five carbons (two from one molecule of triose phosphate and three from the other) are the rearranged using the energy from ATP to create RuBP (the origional 5 carbon molecule).

This is known as the Calvin cycle.

Tuesday, 9 December 2014

The light-dependent reaction in such detail as to show that • light energy excites electrons in chlorophyll • energy from these excited electrons generates ATP and reduced NADP • the production of ATP involves electron transfer associated with the electron transfer chain in chloroplast membranes • photolysis of water produces protons, electrons and oxygen.

Inside a plant cell there are chlorophyll organelles and these contain grana, stacks of thylakoids.

The thylakoids have phospho-lipid membranes which have proteins studded throughout. There are intrinsic proteins which have the pigment chlorophyll attached and these are called photosystems (PS). There are two different types of photosystems because there are two different pigments of chlorophyll which absorb different wavelengths of light, they are PSII and PSI.

When light hits PSII the chlorophyll absorbs protons (light) which energise two electrons. These electrons have so much energy they leave the outer shell (highest energy level) of their atom and become free.

They move to a protein which can take them on- an electron carrier- but are then moved from this to another one and so forth in what is know as an electron transfer chain (ETC). (When every the electrons join a molecule we say the molecule is reduced and when it leaves the molecule is oxidised so you often hear 'the electrons move through the ETC in a series of oxidation reduction reactions).

Each time the electrons move they loose some energy to the proteins this means that 1) the electron will end up attached to PSI at a normal energy level and 2) the ETC will have gained some energy from them; it uses this to change a ADP molecule and a inorganic phosphate into ATP, which moves into the stroma.

The second photosystem absorbs protons and the energy excites the electrons again. The energy is also used to split water into hydrogen and oxygen (and electrons which go to PSII to replace the ones that were energised out). The oxygen is a waste product, but the hydrogen joins up with the excited electrons and a molecule of NADP to form NADPH (reduced NADP) which is carrys the two electrons and hydrogen out of the thylakoids and into the stroma.