Ananna Amin

2.8 Cell Respiration

Cell respiration: substrates and products
[U1: Cell respiration is the controlled release of energy from organic compounds to produce ATP]

Cell respiration is the controlled release of energy, in the form of ATP, from organic compounds in cells, and follows the
equation below:

Glucose + Oxygen −−→ Carbon Dioxide + Water + ATP

C6H12O6 + 6O2 −−→ 6CO2 + 6H2O + 36 ∼ 38 ATP

Cell respiration can follow an aerobic and an anaerobic pathway. The latter creates a much smaller yield of ATP.

Glycolysis

The first stage in cell respiration is glycolysis. Glucose that is present in the cytoplasm of a cell is broken down by a
series of enzymes, to produce two molecules of a simpler compound called pyruvate. As this occurs, there is a net
production of two molecules of ATP.

glucose → 2 pyruvate + 2 ATP

six-carbon sugar 2 × three-carbon sugar

The next stage of cell respiration depends on whether or not oxygen is available.

ATP from cell respiration

[U2: ATP from cell respiration is immediately available as a source of energy in the cell]

ATP (adenosine triphosphate) is a high energy molecule that functions as an immediate source of power for cell
processes

One molecule of ATP contains three covalently linked phosphate groups – which store potential energy in their
bonds
When ATP is hydrolysed (to form ADP + Pi) the energy stored in the phophate bond is released to be used by the
cell
Cell respiration uses energy stored in organic molecules to regenerate ATP from ADP + Pi (via oxidation)

Cells require energy for 3 main reasons:

Synthesizing large molecules (DNA,RNA,Proteins)
Pumping molecules or ions through membranes by active transport
Moving things in a cell

ATP is an energy supply that is immediately available, and it is made by splitting ADP and phosphate. ADP and
phosphate can then be reconverted into ATP by cell respiration.
Anaerobic cell respiration
[U3: Anaerobic cell respiration gives a small yield of ATP from glucose]

Aerobic respiration is the most efficient way of producing ATP. Aerobic respiration is carried out by cells that have
mitochondria and it produces a great deal of ATP.

Pyruvate molecules produced by glycolysis enter the mitochondria and are broken down, or oxidized, in a series of
reactions that release carbon dioxide and water and produce ATP.
In animals, the pyruvate is converted into lactic acid (or lactate)
In plants and yeasts, the pyruvate is converted into ethanol and carbon dioxide
The two pyruvate molecules from glycolysis first lose carbon dioxide and become two molecules of acetyl CoA in the link
reaction. Acetyl CoA then enters a stage called the Krebs cycle and is modified still further, releasing more carbon
dioxide.
Finally, products of the cycle react directly with oxygen and the result is the release of large amounts of ATP. The original
glucose molecule is completely broken down to carbon dioxide and water so the equation for aerobic respiration is often
shown as:

glucose + oxygen → carbon dioxide + water + 38 ATP

C6H12O6 + 6O2 → 6CO2 + 6H2O + 38 ATP

The purpose of anaerobic respiration is to restore stocks of NAD+ – as this molecule is needed for glycolysis

By restoring stocks of NAD+ via anaerobic pathways, the organism can continue to produce ATP via glycolysis

The conversion of pyruvate into lactic acid (animals) or ethanol and CO2 (plants / yeasts) is reversible
 Hence, pyruvate levels can be restored once oxygen is present and a greater yield of ATP may be produced
aerobically

When no oxygen is available to the cells, the following process occurs:

Glycolysis occurs in the cell’s cytoplasm, where a glucose molecule is broken down into two smaller 3-carbon
molecules called pyruvate {It also makes Hydrogen carriers (NADH) from an oxidised precursor (NAD+) & A
small yield of ATP (net gain of 2 molecules)}

In yeast cells, pyruvate is converted into ethanol and carbon dioxide (there is no further yield of ATP and the
products are released as waste). This process is known as fermentation.

In mammalian cells, pyruvate molecules are converted into lactate molecules (also known as lactic acid), with no
further yield of ATP. Lactate accumulates and can lead to changes in pH (lactic acidosis), which can be
dangerous in the long term
Aerobic cell respiration
[U4: Aerobic cell respiration requires oxygen and gives a large yield of ATP from glucose]

Anaerobic respiration occurs in the cytoplasm of cells. In animal cells, the pyruvate produced by glycolysis is
converted to lactate , which is a waste product and is taken out of the cells. In humans, anaerobic respiration occurs if a
person is doing vigorous exercise and their cardiovascular system is unable to supply sufficient oxygen for aerobic
respiration to provide ATP at the necessary rate.
Although anaerobic respiration releases far less energy per molecule of glucose than aerobic respiration, the extra ATP
enables the person to continue exercising for a short period. One consequence of the build-up of lactate in the muscles
that occurs during anaerobic respiration is cramps, so this type of respiration cannot be sustained for very long.

Pyruvate is broken down into carbon dioxide and water, and a large amount of ATP is produced (~34 – 36
molecules)

Although aerobic respiration typically begins with glycolysis in carbohydrates, glycolysis itself is an anaerobic process

Aerobic respiration consists of the link reaction, citric acid cycle (or Krebs cycle) and the electron transport chain
pyruvate → lactate

In other organisms, such as yeast, anaerobic respiration is also known as fermentation, and produces a different
outcome. The pyruvate molecules from glycolysis are converted to ethanol (alcohol) and carbon dioxide .

pyruvate → ethanol + carbon dioxide

No further ATP is produced by the anaerobic respiration of pyruvate, so this type of respiration gives only a small yield of
ATP from glucose.

When oxygen is present, pyruvate can be further broken down in the cytoplasm and enter the mitochondria in the form
of acetyl-CoA (a 2-carbon molecule).

Acetyl-CoA enters the Krebs cycle, where a series of redox reactions lead to the release of carbon dioxide and the
formation of intermediate molecules.

These molecules are used in the electron transport chain (at the mitochondrial membrane), resulting in a large
yield of ATP and the release of water as a by-product
Anaerobic respiration in food production
[A1: Use of anaerobic cell respiration in yeasts to produce ethanol and carbon dioxide in baking]

Anaerobic respiration of yeast has been used in baking and brewing for thousands of years. The strains of yeast used for
baking and brewing are different and each has been selected for its different characteristics. Yeast dies in the high
temperature.

Baking yeasts feed on sugar and our in bread dough and grow more quickly than brewing yeasts, which are slow growing
but able to tolerate higher alcohol concentrations. In yeasts, fermentation results in the production of ethanol and
carbon dioxide – which can be used in food processing:

Bread – Carbon dioxide causes dough to rise (leavening), the ethanol evaporates during baking
Alcohol – Ethanol is the intoxicating agent in alcoholic beverages (concentrations above ~14% damage the yeast)
Bacterial cultures can also undergo fermentation to produce a variety of food products
Yogurt / Cheese – Bacteria produce lactic acid anaerobically, which modifies milk proteins to generate yogurts and
cheeses

[A2:Lactate production in humans when anaerobic respiration is used to maximize the power of muscle
contractions]

Muscle contractions require the expenditure of high amounts of energy and thus require high levels of ATP. When
exercising at high intensity, the cells’ energy demands will exceed what the available levels of O2 can supply
aerobically

Hence the body will begin breaking down glucose anaerobically to maximise ATP production

This will result in an increase in the production of lactic acid, which leads to muscle fatigue
When the individual stops exercising, oxygen levels will increase and lactate will be converted back to pyruvate
Although carbohydrates, lipids and proteins can all be consumed as energy sources, only carbohydrates will typically
undergo anaerobic respiration

How the conditions of cell respiration change with increasing energy demand
 At high intensities, the aerobic consumption of fats is decreased while the anaerobic consumption of sugars
increases
Consequently, lactate levels will increase at higher levels of exercise intensity

Assessing ethics in science – using invertebrates in a respirometer

[S1:Analysis of results from experiments involving measurement of respiration rates in germinating

seeds or invertebrates using a respirometer]

A simple respirometer can be used to monitor respiration in small organisms such as woodlice or in germinating
seeds.The apparatus can demonstrate that oxygen is used and carbon dioxide produced during respiration.

Test organisms are placed in two large boiling tubes as shown, so that one contains living organisms (tube A) and the
other, which acts as a control, contains either dead organisms or is left empty (tube B). Soda lime or another alkali such
as potassium hydroxide absorbs carbon dioxide.As oxygen is used by the living things in tube A, the level of liquid rises
in the arm of the manometer attached to tube A.

If required, measurements of time can be made so that the rate of respiration can be estimated.The temperature in the
apparatus is kept constant by immersing the tubes in a water bath.This minimizes any change in volume due to
temperature change.

Respirometers can be used to perform many experiments:

the respiration rate of different organisms can be compared

the effect of temperature on the respiration rate

respiration rates can be compared in active/inactive organisms

Carbon dioxide production can be measured with a data logger or by pH changes if the specimen is immersed in
water
When an alkali is included to absorb CO2, oxygen consumption can be measured as a change in pressure within the
system
The pressure change can be detected with a data logger or via use of a U-tube manometer

Factors which may affect respiration rates include temperature, hydration, light (plants), age and activity levels

An increase in carbon dioxide levels will indicate an increase in respiration (CO2 is a product of aerobic respiration)

A decrease in oxygen levels will indicate an increase in respiration (O2 is a requirement for aerobic respiration)
2.9 Photosynthesis
Photosynthesis
U1: Photosynthesis is the production of carbon compounds in cells using light energy

Photosynthesis is the process in which plants produce their own organic substances to be used as nutrients.

Animals then consume these organic compounds as food and release the stored energy via cell respiration

Photosynthesis (anabolic synthesis of organic compounds) is essentially the reverse of cell respiration (catabolic
breakdown)

Photosynthetic pigments
U2: Visible light has a range of wavelengths with violet the shortest wavelength and red the longest.

Chloroplasts contain a number of different pigments that are associated with light absorption. Absorption spectra for
two types of chlorophyll and carotenoid pigments found in green plants. Chromatography is a simple technique used to
separate different substances in a mixture and it can be used to separate the pigments in extracts from plant leaves.

[S3: Separation of photosynthetic pigments by chromatograph]

Two techniques are commonly used: paper chromatography, which uses a special high-grade paper with carefully
controlled spaces between the cellulose fibres, and thin-layer chromatography (TLC), which is carried out on a thin plate
of glass or plastic coated with a layer of adsorbent material such as silica gel or cellulose (known as the stationary phase).

During chromatography a solvent moves up the paper or plate by capillary action and carries pigments with it by mass
flow. Smaller molecules are able to move more easily and so can travel further than larger molecules. After a period of
time, photosynthetic pigments from chloroplast extracts become separated and can be compared and measured.

Photosynthetic organisms do not rely on a single pigment to absorb light, but instead benefit from the combined
action of many

These photosynthetic pigments are grouped into photosystems that absorb and funnel light energy
By grouping pigments that have individualised absorption spectra together, the cell maximises its light absorption

When a pigment is energised by light, it releases high energy electrons (ionisation)

Antenna pigments transfer their energised electrons to a central reaction centre
From the reaction centre, electrons are passed on to an acceptor molecule in an electron transport chain to
synthesise ATP

The presence of accessory pigments explains why not all leaves are green

While chlorophyll possesses a green colouration, other pigments (e.g. anthocyanins) may produce different colours
Deciduous trees change colour when leaves stop producing chlorophyll in winter when levels of available light are
low

Light spectrum and chlorophyll

U3: Chlorophyll absorbs red and blue light most effectively and reflects green light more than other
colors.
 Chlorophyll is a green pigment found in photosynthetic organisms that is responsible for light absorption

When chlorophyll absorbs light, it releases electrons which are used to synthesise ATP (chemical energy)

There are a number of different chlorophyll molecules, each with their own absorption spectra, however collectively:

Chlorophyll absorbs light most strongly in the blue portion of the visible spectrum, followed by the red portion
Chlorophyll reflects light most strongly in the green portion of the visible spectrum (hence the green colour of
leaves)

Sunlight is made up of a range of wavelengths including colors red, green and blue within the visible light spectrum. The
smaller the wavelength the more energy is reflected (blue wavelength), and the larger the wavelength the less energy
reflected (red). Green color is reflected from medium wavelengths.

To absorb and reflect these light waves, specific pigments in plants are needed. The main photosynthetic pigment is
chlorophyll; it absorbs red and blue light very well, and reflects mostly green light (thus giving plants their green color).
Chlorophyll is located in clusters inside chloroplasts.
Below is the absorption spectrum of chlorophyll, showing peaks at the wavelengths easily absorbed by the pigment (blue
and red) and a trough on green, the least absorbed wavelength. By looking at the action spectrum (wavelengths of light
most used during the photosynthesis reactions) it is clear why chlorophyll is the main pigment in this process: the
wavelengths readily absorbed by chlorophyll are majorly used in photosynthesis.

Photosynthetic Reaction
U4: Oxygen is produced in photosynthesis from the photolysis of water.

Photosynthesis consists of light-dependent and light-independent reactions. The light dependent reactions result in the
yield of ATP, oxygen and hydrogen.
The light dependent reactions convert light energy from the Sun into chemical energy (ATP)
The light independent reactions use the chemical energy to synthesise organic compounds (e.g. carbohydrates)

Step 1: Light Dependent Reactions

Light is absorbed by chlorophyll, which results in the production of ATP (chemical energy)
Light is also absorbed by water, which is split (photolysis) to produce oxygen and hydrogen
 The hydrogen and ATP are used in the light independent reactions, the oxygen is released from stomata as a waste
product

Step 2: Light Independent Reactions

ATP and hydrogen (carried by NADPH) are transferred to the site of the light independent reactions
The hydrogen is combined with carbon dioxide to form complex organic compounds (e.g. carbohydrates, amino
acids, etc.)
The ATP provides the required energy to power these anabolic reactions and fix the carbon molecules together

Hydrogen and electrons are then involved in the electron transport chain which results in a yield of ATP and
intermediate molecules for the light-independent reactions

The Calvin cycle: using energy to form carbohydrates and other

carbon compounds
U5: Energy is needed to produce carbohydrates and other carbon compounds from carbon dioxide.

The light-independent reactions lead to the formation of complex carbohydrates.

Also known as the Calvin cycle, where ATP and carbon dioxide are used to convert inorganic compounds into organic
compounds. This is achieved by carbon fixation, which requires energy from ATP.

Rate-limiting factors of photosynthesis

U6: Temperature, light intensity and carbon dioxide concentration are possible limiting factors on the
rate photosynthesis.
Light-dependent reactions

The first stage is known as the ‘light-dependent reactions’ because light is essential for them to occur.

Chlorophyll absorbs light energy and this energy is used to produce ATP. The energy is also used to split water molecules
into hydrogen and oxygen in a process called photolysis. Hydrogen ions and electrons (from the hydrogen part of
water) and oxygen are released. Oxygen is a waste product of photosynthesis but is vital to sustain the lives of aerobic
organisms once it has been released into the atmosphere.The ATP, hydrogen ions and electrons are used in the light-
independent reactions

Light-independent reactions

ATP, hydrogen ions and electrons are used in the second stage of photosynthesis, the ‘light-independent reactions’.
During the ‘light-independent reactions’, carbon dioxide, taken in from the environment, is combined with hydrogen and
ATP to form a range of organic molecules for the plant.The conversion of inorganic carbon dioxide to organic molecules
such as glucose is known as carbon fixation.ATP provides the energy for the process.

More oxygen will be produced and more carbon dioxide used.Temperature, light intensity and carbon dioxide
concentration are all possible limiting factors on the rate of photosynthesis. But photosynthesis cannot increase beyond
certain limits. The effect of light, temperature and carbon dioxide in the environment can be measured experimentally,
varying one factor while keeping the others the same.

An increase in light intensity, when all other variables are unchanging, will produce an increase in the rate of
photosynthesis that is directly proportional to the increase in light intensity. However, at a certain light intensity,
enzymes will be working at their maximum rate.

Light Intensity: At low light intensities, rate of photosynthesis is limited. Photolysis, which requires the absorption of
light waves slows down, and thus, so does oxygen and ATP production.

Indirectly limits the light-independent reactions, as ATP is necessary for carbon fixation to occur. The graph levels off
once all the enzymes and reactions are occurring at the highest speed possible. As light intensity increases reaction rate
will increase, as more chlorophyll are being photo-activated

Carbon Dioxide Concentration: Rate-limiting step in the Calvin cycle → carbon cannot be fixed to inorganic
compounds and thus glucose production slows down.
Increasing CO2 concentration increases the rate of photosynthesis, until the photosynthetic enzymes involved in the
cycle (e.g. rubisco) reach their saturation point and can no longer increase reaction rates.

Temperature: At low temperatures, the enzymes involved in photosynthetic reactions work very slowly.

Rate of reaction increases steadily as temperature increases, until reaching an optimum point when all enzymes are
working at a high rate. When the temperature surpasses this optimal point, enzymes can be denatured, once again
decreasing the photosynthetic rate. As temperature increases reaction rate will increase, as reactants have greater kinetic
energy and more collisions result

Oxygenation of Earth
A1: Changes to the Earth’s atmosphere, oceans and rock deposition due to photosynthesis.

These early photosynthetic life forms reduced the carbon dioxide content of the atmosphere and they also started to
produce oxygen. At first, oxygen was taken up by rocks in the Earth’s mantle, where oxygen combined with reduced iron
compounds to form iron oxides.
Approximately 2.3 billion years ago, photosynthetic organisms began to saturate the environment with oxygen

This led to changes in the Earth’s atmosphere, oceans, rock deposition and biological life
Oceans

Earth’s oceans initially had high levels of dissolved iron (released from the crust by underwater volcanic vents)
When iron reacts with oxygen gas it undergoes a chemical reaction to form an insoluble precipitate (iron oxide)
When the iron in the ocean was completely consumed, oxygen gas started accumulating in the atmosphere
Atmosphere

For the first 2 billion years after the Earth was formed, its atmosphere was anoxic (oxygen-free)
 The current concentration of oxygen gas within the atmosphere is approximately 20%
Rock Deposition

The reaction between dissolved iron and oxygen gas created oceanic deposits called banded iron formations (BIFs)
These deposits are not commonly found in oceanic sedimentary rock younger than 1.8 billion years old
This likely reflects the time when oxygen levels caused the near complete consumption of dissolved iron levels
As BIF deposition slowed in oceans, iron rich layers started to form on land due to the rise in atmospheric O2
levels
Biological Life

Free oxygen is toxic to obligate anaerobes and an increase in O2 levels may have wiped out many of these species

Conversely, rising O2 levels was a critical determinant to the evolution of aerobically respiring organisms

With greater availability of oxygen, metabolic pathways became more efficient, and aerobic organisms proliferated in the
oceans. Carbon dioxide removed from the atmosphere ultimately ended up in the shells and decomposed remains of sea
creatures, and built up marine sediments, which eventually became incorporated in sedimentary and, later,
metamorphic rocks.

As oxygen accumulated in the upper atmosphere, sunlight would have been able to act on it and form ozone.The ozone
layer helped to maintain a more stable temperature on earth.

Action Spectrum
S1: Drawing an absorption spectrum for chlorophyll and an action spectrum for photosynthesis

Pigments absorb light as a source of energy for photosynthesis

The absorption spectrum indicates the wavelengths of light absorbed by each pigment (e.g. chlorophyll)
The action spectrum indicates the overall rate of photosynthesis at each wavelength of light

There is a strong correlation between the cumulative absorption spectra of all pigments and the action spectrum
Both display two main peaks – a larger peak at the blue region (~450 nm) and a smaller peak at the red region
(~670 nm)
Both display a trough in the green / yellow portion of the visible spectra (~550 nm)

(Action is the bold line)

S2: Design an experiment to investigate limiting factors on photosynthesis.

Photosynthesis can be measured directly via the uptake of CO2 or production of O2, or indirectly via a change in
biomass

It is important to recognise that these levels may be influenced by the relative amount of cell respiration occurring
in the tissue
Measuring CO2 Uptake

Carbon dioxide uptake can be measured by placing leaf tissue in an enclosed space with water
Water free of dissolved carbon dioxide can initially be produced by boiling and cooling water
Carbon dioxide interacts with the water molecules, producing bicarbonate and hydrogen ions, which changes the
pH (↑ acidity)
Increased uptake of CO2 by the plant will lower the concentration in solution and increase the alkalinity (measure
with probe)
Alternatively, carbon dioxide levels may be monitored via a data logger

Measuring O2 Production

Oxygen production can be measured by submerging a plant in an enclosed water-filled space attached to a sealed
gas syringe
Any oxygen gas produced will bubble out of solution and can be measured by a change in meniscus level on the
syringe
Alternatively, oxygen production could be measured by the time taken for submerged leaf discs to surface
Oxygen levels can also be measured with a data logger if the appropriate probe is available
Measuring Biomass (Indirect)

Glucose production can be indirectly measured by a change in the plant’s biomass (weight)
This requires the plant tissue to be completely dehydrated prior to weighing to ensure the change in biomass
represents organic matter and not water content
An alternative method for measuring glucose production is to determine the change in starch levels (glucose is
stored as starch)
Starch can be identified via iodine staining (turns starch solution purple) and quantitated using a colorimeter
8.1 Metabolism
Metabolic pathways
[U1: Metabolic pathways consist of chains and cycles of enzyme-catalyses reactions]

Metabolic reactions are chemical processes that occur in all cells to keep them alive. Respiration and photosynthesis are
two key metabolic pathways in ecosystems. Light energy from the Sun is trapped as chemical energy in photosynthesis
and then the energy is transferred through food chains and released back to the environment as heat energy from
respiration.

Metabolic pathways consist of chains or cycles of reactions that are catalysed by enzymes. Metabolism includes all the
chemical activities that keep organisms alive. Metabolic pathways may be very complex, but most consist of a series of
steps, each controlled by an enzyme.
Some metabolic pathways consist of chains of reactions (glycolysis), where the initial substrate and end product do not
necessarily interact or resemble one another. Other metabolic pathways consist of cycles of reactions (Krebs cycle),
where a substrate of the cycle is constantly regenerated from other intermediated involved in the same cycle. Many
metabolic pathways include both kinds of reactions.

Enzymes & activation energy of reactions

[U2: Enzymes lower the activation energy of the chemical reactions that they catalyst]

Enzymes are globular proteins that function as biological catalysts that speed up chemical reactions in cells by binding
substrates to their active site. The way enzymes catalyse reactions is as follows:

Before a molecule of the reactant can take part in the reaction, it has to gain energy (aka activation energy), which helps
break the molecular bonds within the reactant.

When new bonds are made after the reactant is broken down, energy is released. Enzymes reduce the activation energy
of the reactions they catalyse by weakingn the reactant’s molecular bonds, making it easier for the reaction to occur.

When an enzyme binds to a substrate it stresses and destabilises the bonds in the substrate
This reduces the overall energy level of the substrate’s transitionary state, meaning less energy is needed to convert
 it into a product and the reaction proceeds at a faster rate

The active site of an enzyme is very important because it can lower the amount of energy needed to reach a transition
state, so the reaction can occur at the temperature of the organism.

Types of Enzymatic Reactions

If the reactants contain more energy than the products, the free energy is released into the system (exergonic)

These reactions are usually catabolic (breaking down), as energy is released from broken bonds within a molecule

If the reactants contain less energy than the products, free energy is lost to the system (endergonic)
These reactions are usually anabolic (building up), as energy is required to synthesise bonds between molecules

Induced- fit model of enzyme action

The lock-and- key hypothesis cannot account for the binding and simultaneous change that is seen in many enzyme
reactions, nor the fact that some enzymes can bind to more than one similarly shaped substrate.

A more likely explanation of enzyme action is that the shape of an enzyme is changed slightly as a substrate binds to its
active site. The substrate causes or induces a slight change in the shape of the active site so it can fit perfectly. As the
enzyme changes shape, the substrate molecule is activated so that it can react and the resulting product or products are
released.The enzyme is left to return to its normal shape, ready to receive another substrate molecule.
Enzymes do not change thequantity of product that is formed, only the rate at which the product is formed.

Competitive vs non-competitive inhibition

[U3: Enzyme inhibitors can be competitive or non-competitive]

Normal Enzyme Reaction

In a normal reaction, a substrate binds to an enzyme (via the active site) to form an enzyme-substrate complex
The shape and properties of the substrate and active site are complementary, resulting in enzyme-substrate
specificity
When binding occurs, the active site undergoes a conformational change to optimally interact with the substrate
(induced fit)
This conformational change destabilises chemical bonds within the substrate, lowering the activation energy
As a consequence of enzyme interaction, the substrate is converted into product at an accelerated rate

Competitive inhibition

A competitive inhibitor competes directly for the active site of the enzyme by binding to it. It prevents the substrate from
binding until the inhibitor dissociates. The inhibitor must have a very similar molecular structure as the substrate in
order to fit the active site and be able to bind to it.

Can be reversible or irreversible.

Increasing substrate concentration can usually reduce the inhibitory effect, as the inhibitor is more readily displaced by
the many substrate molecules.

Competitive Inhibition

Competitive inhibition involves a molecule, other than the substrate, binding to the enzyme’s active site
The molecule (inhibitor) is structurally and chemically similar to the substrate (hence able to bind to the active site)
The competitive inhibitor blocks the active site and thus prevents substrate binding
As the inhibitor is in competition with the substrate, its effects can be reduced by increasing substrate concentration

Example: In the Krebs cycle, succinate dehydrogenase acts on substrate succinate, removing a
hydrogen atom and converting it into another intermediate. Malonate acts as a competitive inhibitor,
effectively slowing down the Krebs cycle.
Non-competitive inhibition

A non-competitive inhibitor binds to the enzyme at a different site from the active site (also known as allosteric site).

Binding of the inhibitor at the allosteric site causes a conformational change in the enzyme (active site included), making
it non-functional and slowing down the reaction.

Usually reversible (not always), but unlike competitive inhibition, increasing substrate concentration does not reduce the
inhibitory effect (even if there are more substrate molecules, they cannot bind to the non-functional active site).

Noncompetitive Inhibition

Non-competitive inhibition involves a molecule binding to a site other than the active site (an allosteric site)
The binding of the inhibitor to the allosteric site causes a conformational change to the enzyme’s active site
As a result of this change, the active site and substrate no longer share specificity, meaning the substrate cannot
bind
As the inhibitor is not in direct competition with the substrate, increasing substrate levels cannot mitigate the
inhibitor’s effect

Example: Nerve gas (Sarin) binds to respiratory enzyme acetyl cholinesterase allosterically, changing the
shape of the enzyme’s active site.

Substrate can no longer bind, and this disruption can result in a blockade of the respiratory pathway → can be lethal, as
this process is irreversible
Examples of Enzyme Inhibition

Enzyme inhibitors can serve a variety of purposes, including in medicine (to treat disease) and agriculture (as
pesticides)

An example of a use for a competitive inhibitor is in the treatment of influenza via the neuraminidase inhibitor,
 RelenzaTM
An example of a use for a non-competitive inhibitor is in the use of cyanide as a poison (prevents aerobic
respiration)

End-product inhibition
[U4: Metabolic pathways can be controlled by end-product inhibition]

End-product inhibition occurs when the product of the last reaction in a metabolic pathway (chain or cycle) inhibits the
enzyme that catalyzes the first reaction.

The inhibitet enzyme is called the allosteric enzyme. Allosteric enzymes have both an active site and an allosteric site.

The end product binds to the allosteric site and changes the shape of the active site, inhibiting the enzyme, this process is
reversible, so when the end product detaches, the reaction continues. Efficient way of controlling metabolic rate. If the
concentration of the product is too high, end-product inhibition stops the pathway, producing less waste.

When the end-product starts to be used up, its inhibiting e ect reduces, the inhibited enzyme is reactivated and
production begins again. This is an example of negative feedback

End-product inhibition (or feedback inhibition) is a form of negative feedback by which metabolic pathways can be
controlled

In end-product inhibition, the final product in a series of reactions inhibits an enzyme from an earlier step in the
sequence
The product binds to an allosteric site and temporarily inactivates the enzyme (via non-competitive inhibition)
As the enzyme can no longer function, the reaction sequence is halted and the rate of product formation is
decreased

End-product inhibition functions to ensure levels of an essential product are always tightly regulated
If product levels build up, the product inhibits the reaction pathway and hence decreases the rate of further product
formation
 If product levels drop, the reaction pathway will proceed unhindered and the rate of product formation will increase

An example of end-product inhibition

[A1: End-product inhibition of the pathway that converts threonine to isoleucine]

Threonine is converted to isoleucine in a series of five enzyme-controlled stages. Isoleucine, as the end product of
threonine metabolism, can inhibit threonine deaminase, the first of the five enzymes in the process.

Isoleucine inhibits the enzyme by binding to the molecule at a site away from the active site.When it is attached, the
active site of the enzyme is changed so that no further substrate can bind to it.As isoleucine concentration increases,
more and more isoleucine molecules attach to this inhibition site on enzyme molecules and therefore inhibit further
production of isoleucine. As their concentration falls, isoleucine molecules detach from the threonine deaminase enzyme
molecules and are used in the cell.

Once the inhibitor has been removed, the active site can bind new substrate and the pathway is reactivated.This
mechanism makes the metabolic pathway self-regulating so that there is always sufficient isoleucine present in the cell.

Isoleucine is an essential amino acid, meaning it is not synthesised by the body in humans (and hence must be
ingested)

Food sources rich in isoleucine include eggs, seaweed, fish, cheese, chicken and lamb

In plants and bacteria, isoleucine may be synthesized from threonine in a five-step reaction pathway
In the first step of this process, threonine is converted into an intermediate compound by an enzyme (threonine
deaminase)
Isoleucine can bind to an allosteric site on this enzyme and function as a non-competitive inhibitor

As excess production of isoleucine inhibits further synthesis, it functions as an example of end-product inhibition
 This feedback inhibition ensures that isoleucine production does not cannibalise available stocks of threonine

Rational Drug Design

[A2 Use of databases to identify potential new anti-malarial drugs]
Malaria is a disease caused by parasitic protozoans of the genus Plasmodium

The life cycle of the parasite requires both a human and mosquito host – hence the disease is transmitted via
mosquito bites
The maturation and development of the parasite in both human and mosquito host is coordinated by specific
enzymes
By targeting these enzymes for inhibition, new anti-malarial drugs and medications can be produced

Scientists have sequenced the genome of infectious species of Plasmodium and used it to determine the parasite’s
proteome
From the proteome, enzymes involved in parasitic metabolism have been identified as potential targets for
inhibition

These enzymes may be screened against a bioinformatic database of chemicals to identify potential enzyme
inhibitors
Once a promising compound is identified, it may be chemically modified to improve its binding affinity and lower its
toxicity
In one particular study, over 300,000 chemicals were screened to identify 19 new chemicals that might function as
inhibitors

An alternative method by which potential new anti-malarial medications can be synthesized is via rational drug design
Rational drug design involves using computer modelling techniques to invent a compound that will function as an
inhibitor
Using combinatorial chemistry, a compound is synthesised that is complementary to the active site of the target
enzyme

Enzyme Kinetics
[S1: Distinguish different types of inhibition from graphs at specified substrate concentration]

Competitive and non-competitive inhibitors effect the kinetics of an enzyme-catalysed reaction in different ways:

Both reduce the rate of reaction by limiting the amount of uninhibited enzyme available for reaction

Competitive Inhibitors
Bind directly to the active site and hence exist in direct competition with the substrate
Increasing substrate levels will increase the likelihood of the enzyme colliding with the substrate instead of the
inhibitor
The maximum rate of enzyme activity (Vmax) can still be achieved, although it requires a higher substrate
concentration

Noncompetitive Inhibitors
Bind to an allosteric site and hence do not exist in direct competition with the substrate
 Increasing substrate concentrations will not effect the level of inhibition caused by the non-competitive inhibitor
The maximum rate of enzyme activity (Vmax) is therefore reduced

Allosterism

Allosteric regulation (allosterism) is the modulation of an enzyme’s activity via the binding of an effector molecule
(ligand) to a site otherthan the enzyme’s active site (an allosteric site)

Allosteric binding causes a conformational change in the enzyme’s structure which affects the enzyme’s affinity for
substrate
Allosteric regulation can be either positive (activation) or negative (non-competitive inhibition)

Positive Allosterism
An example of allosteric activation is seen in the binding of oxygen molecules to haemoglobin
Hemoglobin is composed of four distinct subunits and can bind up to four oxygen molecules (HbO8)

As each oxygen molecule binds, it changes the conformation of haemoglobin and increases its affinity for oxygen
This ensures that haemoglobin will transport the maximum amount of oxygen from oxygen-rich areas (i.e. the
lungs)
Conversely, the release of an O2 molecule decreases haemoglobin’s affinity for oxygen – promoting its release in the
tissues

Negative Allosterism
An example of allosteric inhibition can be seen in any example of non-competitive inhibition
Phosphofructokinase (PFK) is an enzyme involved in the breakdown of glucose during glycolysis (to make ATP)
ATP binds to an allosteric site on PFK and inhibits its activity – preventing glycolysis from occurring
Thus ATP prevents the further production of more ATP when energy stocks are high (end-product inhibition)
When energy stocks are low, there is insufficient ATP to inhibit PFK and glycolysis will be able to proceed
8.2 Cell Respiration
Cell Respiration
[U1: Cell respiration involves the oxidation and reduction of electron carriers ]

Cell respiration is the controlled release of energy, in the form of ATP, from organic compounds in cells.

Chemical energy of organic molecules, (glucose), is made available for use in the living cell. Much of the energy
transferred is lost in the form of heat energy, but cells are able to retain significant amounts of chemical energy in
adenosine triphosphate. ATP, found in all cells, is the universal energy currency in living systems. ATP is a relatively
small, soluble molecule. It is able to move, by facilitated diffusion, from the mitochondria where it is synthesized to all
the very many sites where energy is required, such as ...
in muscles for contraction movements ,
in membranes for active transport
in ribosomes for protein synthesis.
Cell respiration is a redox reaction, which involves the oxidation and reduction of electron carriers NAD+ and FAD at
different stages of this metabolic process (oxidation is the loss of electrons and hydrogen; whereas reduction is the gain
of electrons and hydrogen).

Cell respiration is the controlled release of energy from organic compounds to produce ATP

Anaerobic respiration involves the incomplete breakdown of organic molecules for a small yield of ATP
Aerobic respiration involves the complete breakdown of organic molecules for a larger yield of ATP

The breakdown of organic molecules occurs via a number of linked processes that involve a number of discrete steps

By staggering the breakdown, the energy requirements are reduced (activation energy can be divided across several
steps)
The released energy is not lost – it is transferred to activated carrier molecules via redox reactions (oxidation /
reduction)

S2: Annotation of a diagram of a mitochondrion to indicate the adaptations to its function

Matrix: internal cytosol-like area that contains the enzymes necessary for the Krebs cycle and link reaction
Cristae: tubular regions surrounded by membranes that increase surface area for oxidative phosphorylation and the
electron transport chain
Intermembrane space: this small space between mitochondrial membranes allows for the rapid accumulation of
protons (H+) necessary for chemiosmosis to occur and facilitates phosphorylation
Inner membrane: contains the electron transport chain and ATP synthase, which carry out oxidative phosphorylation
and create a large yield of energy in the form of ATP
Outer membrane: separates the contents of the mitochondrion from the rest of the cell. Permeable to pyruvate, CO2,
O2 and NAD/NADH + H

Stability
[U2: Molecules that have been phosphorylated are less stable]

Phosphorylation is the addition of a phosphate molecule to an organic molecule. The purpose is to make the
phosphorylated molecule more unstable ( more likely to react). Phosphorylation activates the molecule.
Adenosine triphosphate (ATP) is a high energy molecule that functions as an immediate power source for cells

One molecule of ATP contains three covalently bonded phosphate groups – which store potential energy in their
bonds
Phosphorylation makes molecules less stable and hence ATP is a readily reactive molecule that contains high
energy bonds
When ATP is hydrolysed (to form ADP + Pi), the energy stored in the terminal phosphate bond is released for use
by the cell

ATP has two key functions within the cell:

It functions as the energy currency of the cell by releasing energy when hydrolysed to ADP (powers cell
metabolism)
It may transfer the released phosphate group to other organic molecules, rendering them less stable and more
reactive

ATP is synthesised from ADP using energy derived from one of two sources:

Solar energy – photosynthesis converts light energy into chemical energy that is stored as ATP
Oxidative processes – cell respiration breaks down organic molecules to release chemical energy that is stored as
ATP

Glycolysis: from glucose to pyruvate

U3: Glucose is converted to pyruvate during glycolysis, which takes place in the cytoplasm
U4: Glycolysis does not use oxygen and produces a small net gain of ATP

Glycolysis is a chain reaction pathway that is catalysed by enzymes in the cytoplasm of the cell and converts a glucose
molecule into two pyruvates. It uses no oxygen, so it happens in aerobic and anaerobic cell respiration (in both
prokaryotes and eukaryotes). It is divided in four main phases:

Activation / Phosphorylation phase

Two molecules of ATP are used to begin glycolysis. One phosphate from each ATP phosphorylates the glucose molecule
to form intermediate molecule fructose bisphosphate

Lysis phase

This 6-carbon intermediate is split into two 3-carbon sugars, each containing one phosphate group

Oxidation phase

Another phosphorylation takes place but this time an inorganic phosphate ion, Pi, is used and not ATP. Two hydrogen
atoms are removed from each 3-carbon molecule (oxidation). The energy released by this oxidation is used to link
another free phosphate group to each 3-carbon molecule. The hydrogen atoms are then carried by electron carrier NAD+
(forming NADH+H+)

ATP formation phase

Pyruvate is formed by removing the two phosphate groups from each 3-carbom molecules and phosphorylating ADP
(yielding 4 ATP molecules). Because 2 ATP were initially used in the activation phase, glycolysis yields the following net
products:

• 2×ATP
• 2 × pyruvate
• 2 × NADH+H+
The net products of Glycolysis: -2ATP, -2NADH+H+ ,-2Pyruvate
Depending on the availability of oxygen, the pyruvate may be subjected to one of two alternative processes:

Aerobic respiration occurs in the presence of oxygen and results in the further production of ATP (~ 34 molecules)
Anaerobic respiration (fermentation) occurs in the absence of oxygen and no further ATP is produced

Aerobic Respiration

If oxygen is present, the pyruvate is transported to the mitochondria for further breakdown (complete oxidation)
This further oxidation generates large numbers of reduced hydrogen carriers (NADH + H+ and FADH2)

In the presence of oxygen, the reduced hydrogen carriers can release their stored energy to synthesise more ATP
Aerobic respiration involves three additional processes – the link reaction, krebs cycle and the electron transport
chain

Anaerobic Respiration (Fermentation)

If oxygen is not present, pyruvate is not broken down further and no more ATP is produced (incomplete oxidation)
The pyruvate remains in the cytosol and is converted into lactic acid (animals) or ethanol and CO2 (plants and
yeast)
This conversion is reversible and is necessary to ensure that glycolysis can continue to produce small quantities of
 ATP

Glycolysis involves oxidation reactions that cause hydrogen carriers (NAD+) to be reduced (becomes NADH +
H+)
Typically, the reduced hydrogen carriers are oxidised via aerobic respiration to restore available stocks of
NAD+

In the absence of oxygen, glycolysis will quickly deplete available stocks of NAD+, preventing further glycolysis
Fermentation of pyruvate involves a reduction reaction that oxidises NADH (releasing NAD+ to restore
available stocks)
Hence, anaerobic respiration allows small amounts of ATP to be produced (via glycolysis) in the absence of
oxygen

Link reaction and Krebs cycle: Aerobic cell respiration

[U5: In aerobic respiration, pyruvate is decarboxylated and oxidized. In the link reaction, it is converted
to an acetyl compound, then attached to coenzyme A to form acetyl coenzyme A]

[U6: During the Krebs cycle, the oxidation of acetyl groups is coupled with the reduction of hydrogen
carriers and carbon dioxide is released]

If oxygen is readily available to the cell, the pyruvate molecules undergo the link reaction and the Krebs cycle to create a
much higher yield of ATP. Both occur in the mitochondrial matrix.

Link reaction
Pyruvate enters the mitochondrion’s matrix through active transport. In the matrix, enzymes remove hydrogen
(oxidation) and carbon dioxide (decarboxylation) from each pyruvate molecule. This is called oxidative decarboxylation.
Hydrogen is carried away by NAD+. The resulting 2-carbon molecule binds to coenzyme A (CoA), forming end product
acetyl-CoA

1 The link reaction converts pyruvate to acetyl CoA using coenzyme

A, and a carbon atom is removed as carbon dioxide.This is called a decarboxylation reaction.At the same
time as the carbon dioxide is removed, pyruvate is oxidised by the removal of hydrogen.The hydrogen atoms are
removed by NAD+ to form NADH + H+.

2 Acetyl CoA now enters the Krebs cycle to continue the processes of aerobic respiration. Immediately, the
coenzyme A is removed to be recycled.The acetyl component of the acetyl CoA combines with a four-carbon
compound to form the six-carbon compound, citrate.

3, 4 The acetyl (two-carbon) groups are dehydrogenated to release four pairs of hydrogen atoms and decarboxylated to
form two molecules of carbon dioxide so that the two carbons that enter with acetyl CoA leave as carbon dioxide.

5 One molecule of ATP is formed.

 6 Hydrogen is removed during oxidation reactions to the two hydrogen

carriers NAD+ and FAD+.

7 Since the Krebs cycle is a cyclic process, what enters must eventually

leave so that the cycle begins and ends with the same substances.

Link reaction yields:

• 2×CO2

• 2 × NADH+H+

• 2 × acetyl-CoA

Krebs cycle

[In the Krebs cycle, the oxidation of acetyl groups is coupled to the reduction of hydrogen carriers,
liberating carbon dioxide]

Occurs in the matrix of the mitochondrion.

Acetyl-CoA combines with a 4-carbon compound, forming a 6-carbon intermediate (all the products mentioned
below double, since there are two acetyl-CoA molecules that enter the cycle).

The 6-carbon intermediate undergoes oxidative decarboxylation, resulting in a 5-carbon molecule, CO2 and
NADH+H+.

Another oxidative decarboxylation occurs, resulting in a 4-carbon molecule, CO2 and NADH+H+ .
 The 4-carbon intermediate undergoes substrate-level phosphorylation, releasing a phophate group to
phosphorylate an ADP molecule. The resulting intermediate is then oxidized, this time by FAD → FADH2.

The resulting 4-carbon molecule is the same as the starting intermediate that combines with acetyl-CoA at the
beginning of the cycle.

Overall, the two acetyl-CoA molecules lead to the following products:

CO2 is released as a waste product (in total 6 molecules)

Each molecule of glucose forms two molecules of pyruvate during glycolysis, each glucose molecule requires two link
reactions and two rotations of the Krebs cycle. Thus, when working out the products of the cycle we must consider two
sets of products.
• 8 molecules of NADH + H+
• 2 molecules of FADH2
• 2 molecules of ATP
• 6 molecules of CO2
Oxidation

[U7:Energy released during oxidation reactions is carried by reduced NAD and FAD to the cristae of
mitochondria.]

Oxidative phosphorylation the formation of ATP in the mitochondria using energy released by the oxidation of
glucose during respiration.

Cell respiration breaks down organic molecules and transfers hydrogen atoms and electrons to carrier molecules

As the organic molecule is losing hydrogen atoms and electrons, this is an oxidation reaction
Energy stored in the organic molecule is transferred with the protons and electrons to the carrier molecules

The carrier molecules are called hydrogen carriers or electron carriers, as they gain electrons and protons (H+
ions)
The most common hydrogen carrier is NAD+ which is reduced to form NADH (NAD+ + 2H+ + 2e– → NADH +
H+)
A less common hydrogen carrier is FAD which is reduced to form FADH2 (FAD + 2H+ + 2e– → FADH2)

The hydrogen carriers function like taxis, transporting the electrons (and hydrogen ions) to the cristae of the
mitochondria
The cristae is the site of the electron transport chain, which uses the energy transferred by the carriers to
 synthesize ATP
This process requires oxygen to function, and hence only aerobic respiration can generate ATP from hydrogen
carriers
This is why aerobic respiration unlocks more of the energy stored in the organic molecules and produces more ATP

Electron Transport Chain

[U8: The transfer of electrons between carrier molecules in the electron transport chain (ETC) in the
membrane of the cristae is coupled to proton pumps]

Most of the ATP produced from glucose breakdown in the last phase of respiration at the end of the electron
transport chain (ETC). Reactions take place on the inner membrane of the cristae and in the inter-membrane space
between the inner and outer membranes. The inner membrane holds electron carriers, which pick up electrons and
pass them from one to another in a series of oxidations and reductions.

The pathway is called the electron transport chain because electrons from hydrogen are moved along it. The inner
mitochondrial membrane is highly folded into cristae to increase its surface area.The cristae provide a large area for the
protein molecules used in the electron transport chain.

The electron transport chain releases the energy stored within the reduced hydrogen carriers in order to synthesize
ATP

This is called oxidative phosphorylation, as the energy to synthesise ATP is derived from the oxidation of hydrogen
carriers

Oxidative phosphorylation occurs over a number of distinct steps:

Proton pumps create an electrochemical gradient (proton motive force)

 ATP synthase uses the subsequent diffusion of protons (chemiosmosis) to synthesise ATP
Oxygen accepts electrons and protons to form water

Step 1: Generating a Proton Motive Force

The hydrogen carriers (NADH and FADH2) are oxidised and release high energy electrons and protons

The electrons are transferred to the electron transport chain, which consists of several transmembrane carrier
proteins

As electrons pass through the chain, they lose energy – which is used by the chain to pump protons (H+ ions) from
the matrix
The accumulation of H+ ions within the intermembrane space creates an electrochemical gradient (or a proton
motive force)

Electron transport chain and chemiosmosis

[U9: During chemiosmosis protons defuse across the membrane down a concentration gradient via ATP
synthase to produce ATP.]

Electron transport chain and chemiosmosis: ATP

NADH+H+ and FADH2 carry hydrogen and electrons (high in energy) from the mitochondrial matrix to the
mitochondrial inner membrane, where they release H+ ions and electrons. NAD+ allows the production of 3 ATP
molecules and FAD the production of 2 ATP molecules upon entering the electron transport chain.

Electron transport chain and chemiosmosis

Electron carriers are located on the inner mitochondrial membrane, each can receive electrons at different
energy levels.

NADH+H+ and FADH2 are oxidized to the carriers, releasing electrons to the carriers and H+ into the matrix.

Electrons “jump” from one carrier to the next, with each jump releasing some energy.

The energy released allows for the hydrogen ions at the matrix to be pumped into the small intermembrane
space, against their concentration gradient.

At the ennd of the carrier chain, de-energized electrons return to the matrix and join with oxygen and hydrogen
atoms, forming water as a waste product.

At the intermembrane space, hydrogen ions accumulate and the ions begin to move towards enzyme ATP
synthase.
 H+ ions go through ATP synthase, and the enzyme becomes active, allowing for oxidative phosphorylation of
ADP molecules, creating a large yield of ATP (between 36–38) molecules.

Step Two: ATP Synthesis via Chemiosmosis

The proton motive force will cause H+ ions to move down their electrochemical gradient and diffuse back into
matrix
This diffusion of protons is called chemiosmosis and is facilitated by the transmembrane enzyme ATP synthase
As the H+ ions move through ATP synthase they trigger the molecular rotation of the enzyme, synthesising ATP

The Role of Oxygen

[U10: Oxygen binds with free protons to form water, thus maintaining the hydrogen (proton) gradient]

Oxygen is the last electron acceptor in the electron transport chain. The reduction of the oxygen molecule involves both
accepting electrons and forming a covalent bond with hydrogen.

By using the hydrogen, the proton gradient across the inner membrane is maintained so chemiosmosis can continue.

Step Three: Reduction of Oxygen

In order for the electron transport chain to continue functioning, the de-energised electrons must be removed
Oxygen acts as the final electron acceptor, removing the de-energised electrons to prevent the chain from becoming
blocked
Oxygen also binds with free protons in the matrix to form water – removing matrix protons maintains the hydrogen
gradient
In the absence of oxygen, hydrogen carriers cannot transfer energised electrons to the chain and ATP production is
halted

Mitochondria: site for cell respiration

[U11: The structure of mitochondria is closely linked to their function]
Mitochondria are commonly referred to as the “powerhouse” of the cell. This organelle is where the Krebs cycle, electron
transport chain and chemiosmosis occur, making it essential for providing the cell with the energy needed to meet its
functional demands.

Mitochondria are the ‘powerplants’ of the cell – synthesising large amounts of ATP via aerobic respiration

All eukaryotic cells possess mitochondria – aerobic prokaryotes use the cell membrane to perform oxidative
phosphorylation

Mitochondria are thought to have once been independent prokaryotes that were internalised by eukaryotes via
endosymbiosis
They have a double membrane structure (due to vesicular coating as part of the endocytotic process)
They have their own DNA (circular and naked) and ribosomes (70S)
Their metabolic processes are susceptible to certain antibiotics

Decarboxylation:

Carbon atoms are removed from the organic molecule (glucose) to form carbon dioxide
Aerobic respiration involves the complete combustion of glucose (6C) – so six CO2 molecules are produced

Oxidation:

Electrons and hydrogen ions are removed from glucose and taken up by hydrogen carriers (NADH and FADH2)

The hydrogen carriers are in turn oxidised at the electron transport chain (where the energy is used to make ATP)
The electrons and hydrogen ions are then taken up by oxygen (reduction) to form water molecules
Twelve hydrogen carriers are produced and so six oxygen molecules are required (12 × O = 6 × O2)

Phosphorylation:
Energy released from the breakdown of glucose is used to phosphorylate ADP to make ATP
A net total of four ATP molecules are produced directly via substrate level phosphorylation
The remaining ATP is produced indirectly via the electron transport chain (oxidative phosphorylation)

Overall ATP production during aerobic respiration

8.3 Photosynthesis
Photosynthesis
[U1: Light-dependent reactions take place in the intermembrane space of the thylakoids]
[U2: Light –independent reactions take place in the stroma]

Photosynthesis is the process by which cells synthesis organic molecules (e.g. glucose) from inorganic molecules (CO2
and H2O) in the presence of sunlight
This process requires a photosynthetic pigment (chlorophyll) and can only occur in certain organisms (plants, some
bacteria)
In plants, photosynthesis occurs within a specialised organelle called the chloroplast

Photosynthesis is a two step process:

The light dependent reactions convert light energy from the Sun into chemical energy (ATP)
The light independent reactions use the chemical energy to synthesise organic compounds (e.g. carbohydrates)

Step 1: Light Dependent Reactions

Light is absorbed by chlorophyll, which releases energised electrons that are used to produce ATP (chemical
energy)
The electrons are donated to carrier molecules (NADP+), which is used (along with ATP) in the light independent
reactions
The electrons lost from the chlorophyll are replaced by water, which is split (photolysis) to produce oxygen and
hydrogen
The light dependent reactions occur in the intermembrane space of membranous discs called thylakoids

Step 2: Light Independent Reactions

ATP and hydrogen / electrons (carried by NADPH) are transferred to the site of the light independent reactions
The hydrogen / electrons are combined with carbon dioxide to form complex organic compounds (e.g.
carbohydrates)
The ATP provides the required energy to power these anabolic reactions and fix the carbon molecules together
The light independent reactions occur within the fluid-filled interior of the chloroplast called the stroma

Light Dependent Reaction

[U4: Absorption of light by photosystems generates excited electrons]
[U6: Transfer of excited electrons occurs between carriers in thylakoid membranes]

Photosynthesis is the process used by plants to produce their own organic substances (most commonly glucose) using
light energy from the Sun and simple organic substances.
It occurs in green plants, algae and some bacteria. All these organisms are known as autotrophs, which means they can
make their own food.
Photosynthesis can be divided into two parts:
• the light-dependent reactions
• the light-independent reactions.

The light-dependent reactions produce compounds that are used in the light-independent reactions.

Both the light-dependent and the light-independent reactions take place in the chloroplasts of plant cells .The stroma
contains the enzymes required for the light-independent reactions and the stacks of thylakoid membranes increase the
surface area for the light-dependent reactions.

The light-dependent reactions occur on the thylakoid membranes of the chloroplast and are powered by light
energy from the Sun. Each thylakoid is a attend sac so the space in the middle is narrow.The thylakoid membranes form
stacks called grana, which may be joined together by inter-granal membranes. Light is absorbed by photosynthetic
pigments such as chlorophyll, which are found on the granal membranes.

Photosynthesis involves multiple reactions, which can be simply categorized into light-dependent and light-independent.
Light-dependent reactions produce intermediate compounds that are later used in the light-independent reactions to
produce organic “fuels” for the plant.

There are several pigments found in plants and each one absorbs light of a slightly different wavelength.The pigments
are associated with proteins that are involved in electron transport, proton pumping and chemiosmosis.

The light dependent reactions use photosynthetic pigments (organised into photosystems) to convert light energy into
chemical energy (specifically ATP and NADPH)

These reactions occur within specialised membrane discs within the chloroplast called thylakoids and involve three
steps:

Excitation of photosystems by light energy

Production of ATP via an electron transport chain

Reduction of NADP+ and the photolysis of water

Step 1: Excitation of Photosystems by Light Energy

Photosystems are groups of photosynthetic pigments (including chlorophyll) embedded within the thylakoid
membrane
Photosystems are classed according to their maximal absorption wavelengths (PS I = 700 nm ; PS II = 680 nm)
When a photosystem absorbs light energy, delocalised electrons within the pigments become energised or ‘excited'
These excited electrons are transferred to carrier molecules within the thylakoid membrane

Photophosphorylation
[U7: Excited electrons from Photosytem II are used to contribute to generate a proton gradient]
[U8: ATP synthase in thylakoids generates ATP using the proton gradient]

The photosynthetic pigments are combined into two complex groups called photosystems I and II, which absorb the
light energy and use this to boost electrons to a higher energy level so that they become ‘excited’

Step 2: Production of ATP via an Electron Transport Chain

Excited electrons from Photosystem II (P680) are transferred to an electron transport chain within the thylakoid
membrane

As the electrons are passed through the chain they lose energy, which is used to translocate H+ ions into the
thylakoid
This build up of protons within the thylakoid creates an electrochemical gradient, or proton motive force

The H+ ions return to the stroma (along the proton gradient) via the transmembrane enzyme ATP synthase
(chemiosmosis)

ATP synthase uses the passage of H+ ions to catalyse the synthesis of ATP (from ADP + Pi)
This process is called photophosphorylation – as light provided the initial energy source for ATP production
The newly de-energised electrons from Photosystem II are taken up by Photosystem I

Light Independent Reactions

[U9: Excited electrons from Photosytem I are used to reduce NADP]

[U5: Photolysis of water generates electrons for use in the light-independent reactions]

Step 3: Reduction of NADP+ and the Photolysis of Water

 Excited electrons from Photosystem I may be transferred to a carrier molecule and used to reduce NADP+
This forms NADPH – which is needed (in conjunction with ATP) for the light independent reactions
The electrons lost from Photosystem I are replaced by de-energised electrons from Photosystem II
The electrons lost from Photosystem II are replaced by electrons released from water via photolysis
Water is split by light energy into H+ ions (used in chemiosmosis) and oxygen (released as a by-product)

1 The first step in the light-dependent reaction is the photo activation of photosystem II. Pigment molecules in the
photosystem absorb light energy and boost electrons in a molecule of chlorophyll to a higher energy level.The electrons
are accepted by a carrier protein molecule at the start of the electron transport chain.

2 Photosystem II has to replace these lost electrons and it does this by taking them from water.Water is split into
electrons, protons (hydrogen ions) and an oxygen atom. Since the splitting is brought about by light energy, it is called
photolysis.The oxygen is released as an excretory product.

3 Excited electrons travel along the electron transport chain into photosystem I. As they do this, they lose energy but this
is used to pump protons into the thylakoid interior (in a similar way as occurs in the electron transport chain in the
mitochondrion).The thylakoid interior

is small and so a proton concentration gradient builds up quickly. The protons then ow out through a large channel
protein, almost identical to the one in mitochondria, which contains the enzyme ATP synthase.This time though, the
formation of ATP is called photo phosphorylation and it occurs between photosystems II and I .

4 Absorption of light energy causes photoactivation in photosystem I, boosting more electrons to an even higher energy
level.The electrons that arrive from photosystem II replace those that are displaced.The electrons at the higher energy
level are combined with protons in the hydrogen carrier NADP+ to form NADPH + H+.

The two products of the light-dependent reaction, ATP and NADPH + H+, are used to drive the light-independent
reaction.

[U3: Reduced NADP and ATP are produced in the light-dependent reactions]
Cyclic and non-cyclic photo phosphorylation
When ATP is produced using energy from excited electrons owing from photosystem II through photosynthesis I and on
to NADP+, the process is called non-cyclic photophosphorylation.

When light is not a limiting factor, the light-independent reactions may proceed more slowly than the light-dependent
reaction, so that the supply of NADP+ runs out.This means the electrons boosted up from photosystem I have no
acceptor available to take them.They are sent back to photosystem II and rejoin the electron transport chain near the
start, generating more ATP. This alternative pathway is called cyclic photophosphorylation (Figure 8.17) – it
produces neither O2 nor NADPH + H+.

Cyclic Photophosphorylation

Cyclic photophosphorylation involves the use of only one photosystem (PS I) and does not involve the reduction of
NADP+
When light is absorbed by Photosystem I, the excited electron may enter into an electron transport chain to
produce ATP
Following this, the de-energised electron returns to the photosystem, restoring its electron supply (hence: cyclic)

As the electron returns to the photosystem, NADP+ is not reduced and water is not needed to replenish the electron
supply

Non-Cyclic Photophosphorylation

Non-cyclic photophosphorylation involves two photosystems (PS I and PS II) and does involve the reduction of
NADP+
When light is absorbed by Photosystem II, the excited electrons enter into an electron transport chain to produce
ATP
Concurrently, photoactivation of Photosystem I results in the release of electrons which reduce NADP+ (forms
NADPH)
The photolysis of water releases electrons which replace those lost by Photosystem II (PS I electrons replaced by PS
II)

Cyclic vs Non-Cyclic Photophosphorylation

Cyclic photophosphorylation can be used to produce a steady supply of ATP in the presence of sunlight
However, ATP is a highly reactive molecule and hence cannot be readily stored within the cell
Non-cyclic photophosphorylation produces NADPH in addition to ATP (this requires the presence of water)
Both NADPH and ATP are required to produce organic molecules via the light independent reactions
Hence, only non-cyclic photophosphorylation allows for the synthesis of organic molecules and long term energy
storage
De-energized electrons are taken up by photosystem I (PSI), and are once again excited due to the absorption of light and
take up by an electron acceptor. From here, two things may occur:

Electrons enter the electron transport chain once more, to promote further yield of ATP in a process referred to
as cyclic photophosphorylation.

If ATP levels are high enough, electrons are taken up (reduced) electron carrier NADP to form NADPH, and
carried away to the stroma to be used in the light-independent reactions.

Overall, the light-dependent reactions produce:

• ATP
• NADPH

• O2 (released as a by-product)

[U10: In the light-independent reaction a carboxylase catalyzes the carboxylation of ribulose-

bisphosphate]

Light-independent reactions

The light-independent reactions occur in the stroma of the chloroplast and comprise a cyclic pathway called the
Calvin cycle.The pathway is shown in Figure 8.19.ATP and NADPH + H+ formed during the light- dependent stage
supply energy and reducing power for the Calvin cycle. The nal product of the cycle is carbohydrate.

During each turn of the Calvin cycle, one molecule of carbon dioxide is used so Figure 8.19 shows three cycles combined
together.As this is a cycle, what goes in must leave, so three carbons enter in three molecules of carbon dioxide and three
carbons leave in one molecule of triose phosphate, which can be used to form glucose or other organic compounds.

1 At the start of the cycle, the acceptor molecule ribulose bisphosphate (RuBP) combines with incoming carbon
dioxide from the air to form glycerate 3-phosphate (GP).This reaction is called carbon fixation. It is catalysed
by RuBP carboxylase, an enzyme that is sometimes called Rubisco.

The light independent reactions use the chemical energy derived from light dependent reactions to form organic
molecules

The light independent reactions occur in the fluid-filled space of the chloroplast called the stroma

The light independent reactions are collectively known as the Calvin cycle and involve three
main steps:
Carboxylation of ribulose bisphosphate
Reduction of glycerate-3-phosphate
Regeneration of ribulose bisphosphate

Step 1: Carbon Fixation

The Calvin cycle begins with a 5C compound called ribulose bisphosphate (or RuBP)
An enzyme, RuBP carboxylase (or Rubisco), catalyses the attachment of a CO2 molecule to RuBP

The resulting 6C compound is unstable, and breaks down into two 3C compounds – called glycerate-3-
phosphate (GP)
A single cycle involves three molecules of RuBP combining with three molecules of CO2 to make six molecules of
GP

[U11: Glycerinate 3-phosphate is reduced to triose phosphate using a reduced NADP and ATP]

2 The ATP and NADPH + H+ from the light-dependent reaction convert the glycerate 3-phosphate into triose
phosphate (TP). Glycerate 3-phosphate therefore becomes reduced to triose phosphate. No more phosphate is
added so the only input from ATP is energy.

Step 2: Reduction of Glycerate-3-Phosphate

Glycerate-3-phosphate (GP) is converted into triose phosphate (TP) using NADPH and ATP
Reduction by NADPH transfers hydrogen atoms to the compound, while the hydrolysis of ATP provides energy
Each GP requires one NADPH and one ATP to form a triose phosphate – so a single cycle requires six of each
molecule

[U12: Triose phosphate is used to regenerate RuBP and produce carbohydrates]

 [U13: Ribulose bisphosphate is reformed using ATP]

3 Six molecules of triose phosphate are produced but only ve are needed to reform the ribulose bisphosphate to
keep the cycle going. The extra triose phosphate leaves the cycle and is used to synthesise organic molecules
such as glucose or amino acids.

4 Since the triose phosphate that leaves the cycle takes a phosphate with it, this is replaced in the cycle with a
phosphate from ATP, as the ve remaining triose phosphates are converted back to three ribulose bisphosphate
molecules, and the cycle begins again.

Six ‘turns’ of the Calvin cycle produces two triose phosphate molecules, which can be combined to form the nal product,
glucose. Some triose phosphate molecules will follow other pathways to make other organic carbohydrate molecules,
such as sucrose or cellulose, or other molecules that the plant needs, such as amino acids, fatty acids or vitamins.

Step 3: Regeneration of RuBP

Of the six molecules of TP produced per cycle, one TP molecule may be used to form half a sugar molecule
Hence two cycles are required to produce a single glucose monomer, and more to produce polysaccharides like
starch
The remaining five TP molecules are recombined to regenerate stocks of RuBP (5 × 3C = 3 × 5C)
The regeneration of RuBP requires energy derived from the hydrolysis of ATP

Below is an explanation of the light-independent reactions, which take place in the chloroplast’s stroma and are
commonly known as the Calvin cycle, producing glucose and other organic compounds:

Products made in the light-dependent reactions (ATP and NADPH), as well as carbon dioxide molecules that diffuse into
the chloroplast move to the stroma.

The cycle begins and ends with 3 5-carbon molecules called ribulose bisphosphate (RuBP).

RuBP undergoes carbon fixation with the aid of enzyme rubisco, which catalyzes the molecules’ carboxylation using
three carbon dioxide molecules. This yields 3 6-carbon intermediate molecules.

These intermediate molecules are so unstable that they immediately split into 6 3-carbon molecules called glycerate-3-
phosphate (G3P).

G3P is reduced by NADPH and phosphorylated bu ATP, yielding 6 3-carbon triose phosphate (TP) molecules.

One TP molecule leaves the cycle and can be synthetisized into glucose and other organic compounds as the cycle is
repeated and TP accumulates.

The remaining five TP molecules are phospholurated by ATP adn rearranged back into the intial 3 RuBP molecules the
cycle started with

Calvin Cycle

[A1: Calvin’s experiment to elucidate the carboxylation of RuBP]

 The light independent reactions are also collectively known as the Calvin cycle – named after American chemist
Melvin Calvin

Calvin mapped the complete conversion of carbon within a plant during the process of photosynthesis

Calvin’s elucidation of photosynthetic carbon compounds is commonly classed the ‘lollipop experiment’
This is due to the fact that the apparatus he utilised was thought to resemble an upside-down lollipop

Lollipop Experiment

Radioactive carbon-14 is added to a ‘lollipop’ apparatus containing green algae (Chlorella)

Light is shone on the apparatus to induce photosynthesis (which will incorporate the carbon-14 into organic
compounds)
After different periods of time, the algae is killed by running it into a solution of heated alcohol (stops cell
metabolism)
Dead algal samples are analysed using 2D chromatography, which separates out the different carbon compounds
Any radioactive carbon compounds on the chromatogram were then identified using autoradiography (X-ray film
exposure)
By comparing different periods of light exposure, the order by which carbon compounds are generated was
determined
Calvin used this information to propose a sequence of events known as the Calvin cycle (light independent
reactions)

Key Events of the Calvin Cycle

The Calvin cycle outlines the events that result in the formation of organic molecules from inorganic sources (CO2)
 Ribulose bisphosphate (RuBP) is carboxylated by carbon dioxide (CO2) to form a hexose biphosphate compound

The hexose biphosphate compound immediately breaks down into molecules of glycerate-3-phosphate (GP)
The GP is converted by ATP and NADPH into molecules of triose phosphate (TP)
TP can be used to form organic molecules or can be recombined by ATP to reform stocks of RuBP

Chloroplasts
[U14: The structure of the chloroplast is adapted to its function in photosynthesis]

Chloroplasts: the site for photosynthesis

Chloroplasts are the ’solar energy plants’ of a cell – they convert light energy into chemical energy

This chemical energy may be either ATP (light dependent) or organic compounds (light independent)
Only photosynthetic tissue possess chloroplasts (e.g. is present in leaves but not roots of plants)

Chloroplasts are thought to have once been independent prokaryotes that were internalised by eukaryotes via
endosymbiosis
They have a double membrane structure (due to vesicular coating as part of the endocytotic process)
They have their own DNA (circular and naked) and ribosomes (70S)
Their metabolic processes are susceptible to certain antibiotics
Thylakoids: the small, disc-shaped structures increase the surface area for light absorption by photosystems I and II

Thylakoid space: the small space inside thylakoids allows for more rapid accumulation of protons to create a
concentration gradient for chemiosmosis

Stroma: cytosol-like substance where all the enzymes needed for the Calvin cycle are found

Double membrane: isolates the working parts of enzymes within the chloroplasts from the surrounding cytosol

Lamella: connect granules and further increase surface area for light absorption

Grana – thylakoids are arranged into stacks to increase SA:Vol ratio of the thylakoid membrane

[S1: Annotation of a diagram to indicate the adaptations of a chloroplast to its function]

State that the discovery of the radioactive 14C isotope allowed Calvin to determine the pathway of the
light independent reactions of photosynthesis.

By exposing the cells to 14 CO2 for progressively shorter periods of time, Calvin identi ed glycerate 3-phosphate as the rst
stable intermediate in the process and subsequently other labelled sugar phosphates were found to be produced as a
result of its reduction.

From the distribution of 14C in all the labelled compounds, ribulose bisphosphate was eventually identi ed as the
acceptor of carbon dioxide. This nal piece of the cycle explained the labelling patterns of the all the other intermediates.