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Biology Year 2

Energy Transfer in and Between Organisms


Overview of Photosynthesis:
- Photosynthesis uses light energy to combine carbon dioxide and water to form glucose
and oxygen.
- Carbon dioxide + water > glucose + oxygen. The conditions above the arrow are
sunlight and chlorophyll.
- 6CO2 + 6H2O > C6H12O6 + 6O2.

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- Light energy is absorbed by chlorophyll which is found in chloroplasts in some plant cells
and algae.

- The rate of photosynthesis may be limited by the light intensity, temperature or carbon
dioxide concentration.
- The equation is highly simplified as photosynthesis is a complex metabolic pathway
involving many intermediate reactions. It is a process of energy transferral in which some
of the energy in the light is conserved in the form of chemical bonds.

- There are three main stages to photosynthesis;

1. Capturing of light energy - by chloroplast pigments such as

2. The light-dependant reaction - which only occurs

during daylight, in which some of the light energy
absorbed is conserved in chemical bonds. During the
process, an electron flow is created by the eect of light
on chlorophyll, causing water to split in photolysis into
protons (hydrogen ions), electrons and oxygen. The
products are reduced NADP, ATP and oxygen.

3. The light-independent reaction - which may

continue in the dark, in which these protons (hydrogen
ions) are used to produce sugars and other organic molecules.
- All plant cells respire all the time, while only those plant cells with
chloroplasts carry out photosynthesis - and then only in the light.

- Photosynthesis is an example of a metabolic pathway - the process occurs in a series of

small reactions controlled by enzymes.

The Importance of Photosynthesis:

- The energy we rely on has been captured by photosynthesis by sunlight.
- Photosynthesis also produces the oxygen we breathe by releasing it from water molecules.
- In plants, energy in light is absorbed by chlorophyll and then transferred into the chemical
energy of the molecules formed during photosynthesis. Energy is stored in glucose until
the plants release it by respiration to produce ATP during respiration. Plants are
therefore photoautotrophs as they are organisms that can make their own food using light

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- Non-photosynthetic organisms (heterotrophs), feed on the molecules produced by plants
and then also use them to make ATP during respiration. Animals obtain glucose by eating
plants or by eating other animals that have eaten plants, then respire the glucose to
release energy.
- Plants and animal cells need energy for biological processes to occur.
- Plants need energy for things like photosynthesis, active transport, DNA replication, cell
division and protein synthesis.

- Animals need energy for things like muscle contraction, maintenance of body
temperature, active transport, DNA replication, cell division and protein synthesis.

The Leaf:
- The leaf is the main photosynthetic structure in eukaryotic plants.
- Chloroplasts are the cellular organelles within the leaf where photosynthesis takes place.
- Leaves are adapted to bring together the three raw materials of photosynthesis (water,
carbon dioxide and light), and remove its products (oxygen and glucose).
- Leaves have a large surface area that
absorbs as much sunlight as
- The arrangement of the leaves on
the plant minimises overlapping and
so avoids the shadowing of one leaf
by another.

- Leaves are thin, as most light is

absorbed in the first few
micrometers of the leaf and the
diusion distance for gases is kept

- They have a transparent cuticle and epidermis that let light through to the photosynthetic
mesophyll cells beneath.
- They have long, narrow upper palisade mesophyll cells that are packed with chloroplasts
that collect sunlight.
- Leaves have numerous stomata for gaseous exchange so that all mesophyll cells are only a
short diusion pathway from one.
- These stomata open and close in response to changes in light intensity.

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- There are many air spaces in the lower mesophyll layer to allow rapid diusion in the gas
phase of carbon dioxide and oxygen.

- There is a network of xylem that brings water to the leaf cells, and phloem that carries
away the sugars produced during photosynthesis.

- In eukaryotic plants, photosynthesis takes place within cell organelles called chloroplasts.
- They vary in shape and size but are typically disc-
shaped, 2-10um long and 1um in diameter.
- They are surrounded by a double membrane. The
inner membrane is folded into lamellae which
provides a large surface area.

- Within the inner membrane are thylakoids, which

are where the light-dependant stage of
photosynthesis takes place as these contain
photosynthetic pigments e.g. chlorophyll a,
chlorophyll b and carotene. These are coloured
substances that absorb the light energy needed for
photosynthesis. They are attached to proteins. The
protein and pigment is called a photosystem.
- There are two photosystems used by plants to capture light energy. Photosystem I (PSI)
absorbs light best at a wavelength of 700nm and photosystem II (PSII) absorbs light best
at 680nm.
- Thylakoids are stacked into around 100 disc-like structures into a granum (plural grana),
and some thylakoids have tubular extensions that join up with thylakoids in adjacent
grana. These are called intergranal lamellae. The grana is the site of light absorption and
ATP synthesis.

- The stroma is a fluid filled matrix where the light-independent stage of photosynthesis
takes place. This contains enzymes needed for the production of carbohydrates, and a
number of other structures such as starch grains, DNA, and prokaryote ribosomes.
Carbohydrates produced by photosynthesis and not used straight away are stored as starch
grains in the stroma.

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The Light Dependant Reaction:
- When a chlorophyll molecule absorbs light energy, it boosts the energy of a pair of
electrons within this chlorophyll molecule, raising them to a higher energy level.
- The electrons become so energetic that they leave the chlorophyll molecule altogether,
leaving the chlorophyll molecule ionised in a process called photoionisation.
- The energy resulting from the photoionisation of chlorophyll is used for
photophosphorylation - making ATP from ADP and Pi, making reduced NADP
(NADPH) from NADP, and splitting water into protons, electrons and oxygen in
- The light dependent reaction includes two types of photophosphorylation - non-cyclic
and cyclic. Each of these processes has dierent products.

Oxidation and Reduction:

- When a substance gains oxygen or loses hydrogen, the process is called oxidation. The
substance to which the oxygen has been added or hydrogen has been lost is said to be
- When a substance loses oxygen, or gains hydrogen, the process is called reduction.
- In practice, when a substance is oxidised, it loses electrons and when it is reduced it gains
- Oxidation results in energy being given out, whereas reduction results in it being taken in.
- Oxidation and reduction always take place together

Non-Cyclic Photophosphorylation:
- Non-cyclic photophosphorylation produces ATP, reduced NADP and oxygen O2.
- Photosystems in the thylakoid membranes are linked by electron carriers which are
proteins that transfer electrons. The photosystems and electron carriers form an electron
transport chain which is a chain of proteins through which excited electrons flow.
- There are several processes going on all at once in non-cyclic photophosphorylation.
1. Light energy excites electrons in chlorophyll:

Light energy is absorbed by PSII and this excites electrons in chlorophyll. The
electrons move to a higher energy level as have more energy, and these high energy

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electrons are released from the chlorophyll and move down the electron transport
chain to PSI.

The electrons that leave the chlorophyll are taken up by a molecule called an electron

Having lost a pair of electrons, the chlorophyll molecule has been oxidised, and the
electron carrier, which has gained electrons, has been reduced.

The electrons are now passed along a number of electron carriers in a series of
oxidation-reduction reactions. These electron carriers form a transfer chain that is
located in the membranes of the thylakoids.

2. Photolysis of water produces protons, electrons and oxygen:

As the excited electrons from chlorophyll leave PSII to move down the electron
transport chain, they must be replaced if the chlorophyll molecule is to continue
absorbing light energy.

Light energy splits water into protons (H+ ions), electrons and oxygen - this is

2H2O > 4H+ + 4e- + O2

The oxygen by-product from the photolysis of water is either used in respiration or
diuses out of the chloroplast and out of the leaf as a waste product of photosynthesis.

3. Energy from the excited electrons makes ATP:

The excited electrons lose energy as they move down the electron transport chain, and
this energy is used to transport protons (H+ ions) into the thylakoid so that the
thylakoid has a higher concentration of protons than the stroma.

This forms a proton gradient across the thylakoid membrane. Protons move down
their concentration gradient, into the stroma, via the enzyme ATP synthase, which is
embedded in the thylakoid membrane as channel proteins. The rest of the membrane
is impermeable to protons, and these channels form small granules on the membrane
surface and so are known as stalked granules..

As the protons pass through these ATP synthase channels, they cause changes to the
structure of the enzyme which then catalyses the combination of ADP with inorganic
phosphate to form ATP.

The energy from this movement combines ADP and inorganic phosphate Pi to form

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The process of electrons flowing down the electron transport chain and creating a
proton gradient across the membrane to drive ATP synthesis is called chemiosmosis. It
is described by the chemiosmotic theory.

4. Energy from the excited electrons generates reduced NADP:

Light energy is absorbed by PSI, which excites the electrons again to an even higher
energy level. Finally, the electrons are transferred to NADP, along with a proton
from the stroma, to form reduced NADP.

The protons come out of the thylakoid space through the ATP synthase channels and
are taken up by an electron carrier called NADP, which becomes reduced on taking
up the protons.

The reduced NADP is the main product of the light-dependant stage of

photosynthesis and it enters the light-independent reaction, taking with it the
electrons from the chlorophyll molecules.

The reduced NADP is important as it is a further potential source of chemical energy

to the plant.

Cyclic Photophosphoryation:

- Cyclic photophosphorylation produces ATP and only uses PSI.

- It is called cyclic as the electrons from the chlorophyll molecule are not passed onto
NADP, but are passed back to the PSI via electron carriers.
- This means that the electrons are recycled and can repeatedly flow through PSI.
- This process doesn't produce any reduced NADP or oxygen - it only produces small
amounts of ATP.
- ATP is formed in the same way in cyclic photophosphorylation as in non-cyclic
photophosphorylation - by the movement of protons across the thylakoid membrane.

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Comparing Non-Cyclic and Cyclic Photophosphorylation:

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Site of the Light-Dependent Reaction:

- The light-dependant reaction of photosynthesis takes place in the thylakoids of

- The thylakoids are disc-like structures that are stacked together in groups called grana.
- Chloroplasts are structurally adapted to their function of capturing sunlight and carrying
out the light-dependent reaction of photosynthesis in the following ways:

The thylakoid membranes provide a LSA for the attachment of chlorophyll, electron
carriers and enzymes that carry out the light dependant reaction.

A network of proteins in the grand hold the chlorophyll in a very precise manner that
allows maximum absorption of light.

The granal membranes have ATP synthase channels within them, which catalyse the
production of ATP. They are also selectively permeable which allows establishment of
a proton gradient.

Chloroplasts contain both DNA and ribosomes so they can quickly and easily
manufacture some of the proteins involved in the light-dependant reaction.

The Light-Independent Reaction:

- The products of the light-dependent reaction of photosynthesis , namely ATP and
reduced NADP, are used to reduce glycerate 3-phosphate in the second stage of
- Unlike the first stage, this stage doesnt require light directly and, in theory, occurs
whether or not light is available, so it is called the light-independent reaction.
- In practice, it requires the products of the light dependent stage and so rapidly ceases
when light is absent.
- The light-independent reaction takes place in the stroma of the chloroplasts.
- The details of this stage were worked out by Melvin Calvin and his co-workers and so is
referred to as the Calvin cycle.
- It makes a molecule called triose phosphate from carbon dioxide and ribulose
- Triose phosphate can be used to make glucose and other useful substances.
- There are a few steps to the cycle, and it needs ATP and H+ ions to keep it going.

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- The reactions are linked in a cycle, which means the starting compound, ribulose
bisphosphate is regenerated.

- It is really important that RuBP is regenerated, as if it wasn't then glycerate 3-phosphate

wouldn't be formed, the Calvin cycle would stop and photosynthesis would be unable to
- The Calvin Cycle is also called carbon fixation as carbon from CO2 is fixed into an
organic molecule.

- It can be summarised as INPUTS: CO2, ATP, Reduced NADP > OUTPUTS: Organic
Substances, RuBP.

1. Formation of glycerate 3-phosphate:

CO2 from the atmosphere diuses into the leaf through stomata and dissolves in water
around the walls of the mesophyll cells. It then diuses through the cell-surface
membrane, cytoplasm and chloroplast membranes into the stroma of the chloroplast.

In the stroma, the CO2 reacts with the 5-carbon compound ribulose bisphosphate
(RuBP). This reaction is catalysed by the enzyme rubisco (one of the slowest working
enzymes in the natural world), producing an unstable 6-carbon compound which

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quickly breaks down into two molecules of a 3-carbon compound called glycerate 3-
phosphate (GP).


2. Formation of triose phosphate:

The hydrolysis of ATP from the light-dependent reaction provides energy to reduce the
3-carbon compound GP to a dierent 3 carbon compound called triose phosphate (TP).

This reaction also requires H+ ions, which come from reduced NADP (also from the
light-dependent reaction). The NADP is reformed and goes back to the light-
dependent reaction to be reduced again by accepting more protons.

3. Regeneration of ribulose bisphosphate:

Some triose phosphate molecules are converted to useful organic compounds that the
plant requires like starch, cellulose, lipids, glucose, amino acids and nucleotides, but
most triose phosphate molecules continue in the Calvin cycle to regenerate RuBP using
the rest of the ATP from the light dependant reaction.

Site of the Light-Independent Reaction:

- The light-independent reaction of photosynthesis takes place in the stroma of the
- The chloroplast is adapted to carrying out the light-independent reaction of
photosynthesis in the following ways:

The fluid of the stroma contains all the enzymes needed to carry out the light-
independent reaction. Stromal fluid is membrane-bound in the chloroplast which
means a chemical environment which has a high concentration of enzymes and
substrates can be maintained within it - as distinct from the environment of the

The stroma fluid surrounds the grana and so the products of the light-dependant
reaction in the grana can readily diuse into the stroma.

It contains both DNA and ribosomes so it can quick and easily manufacture some of
the proteins involved in the light-independent.

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Hexose Sugars:
- Hexose sugars are simple 6-carbon sugars, like glucose. One hexose sugar is made by
joining two molecules of triose phosphate (TP) together. Hexose sugars can be used to
make larger carbohydrates.
- The Calvin cycle needs to turn six times to make one hexose sugar, as three turns of the
cycle produces six molecules of triode phosphate (as two molecules of TP are made for
every one CO2 molecule used. Five out of six of these TP molecules are used to regenerate
RuBP, so for three turns of the cycle, only one TP is produced thats used to make a hexose
- A hexose sugar has six carbons though, so two TP molecules are needed to form one
hexose sugar, so the cycle must turn six times to produce two molecules of TP that can be
used to make one hexose sugar.

- Six turns of the cycle need 18 ATP and 12 reduced NADP from the light-dependent
- This might seem a bit inecient, but it keeps the cycle going and makes sure theres
always enough RuBP ready to combine with CO2 taken in from the atmosphere.

Carbohydrates, Lipids and Proteins:

- The Calvin Cycle is the starting point for making all the organic substances a plant needs.
- Triode phosphate and glycerine 3-phosphate molecules are used to make carbohydrates,
lipids and amino acids.
- Carbohydrates - hexose sugars are made from two TP molecules and larger carbohydrate
are made by joining hexose sugars together in dierent ways.
- Lipids - these are made using glycerol, which is synthesised from triose phosphate and
fatty acids, which are synthesised from glycerine 3-phosphate.
- Amino acids - some amino acids are made from glycerate 3-phosphate.

Optimum Conditions for Photosynthesis:

- The ideal conditions for photosynthesis vary from one plant species to another, but the
conditions below would be ideal for most plant species in temperature climates like the

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1. High light intensity of a certain wavelength:

Light is needed to provide the energy for the light-dependant reaction, and the higher
the intensity of the light, the more energy it provides.

Only certain wavelengths of light are used for photosynthesis as the photosynthetic
pigments chlorophyll a, chlorophyll b and carotene only absorb the red and blue light in

Green light is reflected, which is why plants look green.

2. Temperature around 25C:

Photosynthesis involves enzymes such as ATP synthase and rubisco.

If the temperature falls below 10C then the enzymes become inactive, but if the
temperature is more than 45C then they may start to denature.

When an enzyme becomes denatured, the bonds holding its tertiary structure together
break, and it loses its 3D shape so the active site wont fit the substrate and the enzyme
can no longer function as a catalyst.

Also, at high temperatures the stomata (pores in the epidermis of a plant that allow gas
exchange) close to avoid losing too much water, which causes photosynthesis to slow
down as less CO2 enters the leaf when the stomata are closed.

3. Carbon dioxide at 0.4%:

Carbon dioxide makes up 0.04% of the gases in the atmosphere.

Increasing this to 0.4% gives a higher rate of photosynthesis, but any higher and the
stomata will start to close.

4. Water:

Plants also need a constant supply of water - too little and photosynthesis will stop, but
too much and the soil becomes waterlogged which reduces the uptake of minerals such
as magnesium, which is needed to make chlorophyll a. This is because there is less
oxygen in waterlogged soil, so roots are unable to respire aerobically, so there is less ATP
available for the active transport of minerals into roots.

Limiting Factors of Photosynthesis:

- Light, temperature and carbon dioxide can all limit photosynthesis. All three of these
things need to be at the right level to allow a plant to photosynthesise as quickly as

- A limiting factor is a variable that can slow down the rate of a reaction.

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- If any one of these factors is too low or too high, it will limit photosynthesis and slow out

- Even if the other two factors are at the perfect level, it wont make any dierence to the
speed of photosynthesis as long as that factor is at the wrong level.
- However, any of these factors could become the limiting factor, depending on the
environmental conditions.

Increasing Plant Growth:

- Agricultural growers know the factors that limit photosynthesis and therefore limit plant
growth. This means they try to create an environment where plants get the right amount
of everything that they need, which increases growth and so increases yield.
- Growers create optimum conditions in glasshouses.
- CO2 CONCENTRATION: carbon dioxide is added to the air, e.g. by burning a small
amount of propane in the carbon dioxide generator.
- LIGHT: light can get in through the glass, and lamps provide light at night time.
Remember that the wavelength of light is also important, so growers will often use red or
blue lights to maximise photosynthesis. If they used green light then it would be reflected
by the plants.
- TEMPERATURE: glasshouses trap heat energy from sunlight which warms the air.
Heaters and cooling systems can also be used to keep a constant optimum temperature,
and air circulation systems make sure the temperature is even throughout the glasshouse.