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Biology
Unit 2
Summary
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 Photosynthesis
Photosynthesis Video https://www.youtube.com/watch?
v=CMiPYHNNg28&ab_channel=AmoebaSisters

 Photosynthesis is the process that combines Carbon Dioxide with Water to form
Glucose and Oxygen.


 The oxygen formed is released through the stomata and the glucose is used in
respiration to produce energy.
 The energy can be used for active transport of mineral ions, DNA replication and
protein synthesis.

Dicotyledonous Leaf
 Diagram Showing the Cross-Sectional Diagram of a Leaf

A Dicotyledonous leaf typically consists of three main parts:

The Epidermis (Upper & Lower)

- The epidermis is the outermost layer

- Usually coated with a waxy cuticle that helps to reduce water loss.

The Mesophyll

- The mesophyll is the inner layer and is composed of two layers:

 The Palisade Mesophyll Layer (made up of palisade parenchyma cells)
This is the main photosynthetic tissue. It contains chloroplast
 The Spongy Mesophyll Layer (made up of spongy parenchyma cells)
Photosynthetic tissue that contains less chloroplasts than the palisade
layer.

The Vascular Bundle

- The vascular bundle contains:

 The Xylem Tissues - Transports water and mineral salts to the leaf
 The Phloem Tissues - Transports sugars throughout the plant
Palisade Cell

Palisade Cells are;

- Long and narrow

- Cylindrically shaped
- Arranged vertically in the leaf

 Palisade cells are specialized plant cells that are found in the upper layer of the
mesophyll in dicotyledonous leaves.
 Palisade cells contain many chloroplasts, which are responsible for carrying out
photosynthesis.
 It is the Primary Site for photosynthesis in a plant as it;
o Contain many closely packed grana (stacks of thylakoid membranes, where
light-dependent reactions occur)
o The grana are surrounded by a fluid-filled stroma where light-independent
reactions occur

Mitochondria occupy the periclinal and anticlinal regions of palisade cells

Chloroplast

Chloroplasts are organelles found in plant cells that are responsible for carrying out
photosynthesis.

 Shaped like flattened discs

Composed of an:

 An Outer membrane
 An inner membrane
 A thylakoid membrane system

 Organelle within plant cells where photosynthesis occurs

 Double membrane envelope surrounding the stroma
 Contains chlorophyll pigments that absorb light energy and convert it into chemical
energy
 Thylakoid membranes within the stroma provide a large surface area for light
absorption
 Chloroplasts are mobile within plant cells and can move to areas where light is more
intense.

Photo-phosphorylation

Photo-phosphorylation is the process that converts light energy into chemical energy in the
form of ATP. Chlorophyll and electron carriers play a crucial role in this process, which also
involves the reduction of NADP and the formation of Oxygen as a by-product.

NOTE: Cyclic Photo-phosphorylation and Non-Cyclic Photo-phosphorylation

are two different mechanisms of the Light-Dependent Stage

There are two types of Photo-phosphorylation:

1. Cyclic Photo-Phosphorylation - Occurs in the thylakoid membranes of chloroplasts and
involves only photosystem I (PSI)

Stages of Cyclic Photo-Phosphorylation

 Light energy is absorbed by chlorophyll, in PSI.

 This causes electrons in the pigments to become excited and move to a higher energy
level, leaving behind a positive charge.
 These excited electrons are passed along a chain of electron carriers in a series of
redox reactions, releasing energy as they go.
 Instead of being passed on to NADP+ to produce NADPH, the high-energy electrons
return to PSI via a different electron carrier.
 The electrons are then re-energized by light energy and passed along the same chain
of electron carriers in a cyclic fashion.
 As the electrons pass through the electron transport chain, they pump protons (H+)
from the stroma into the thylakoid space, creating a proton gradient.
 The proton gradient drives the synthesis of ATP, by ATP synthase (the enzyme that
directly generates ATP), which couples the movement of protons back into the stroma
with the synthesis of ATP from ADP and inorganic phosphates.
 The ATP produced by cyclic photophosphorylation can be used in the light-
independent stage of photosynthesis to power the production of organic molecules.

2. Non-Cyclic Photo-phosphorylation
Stages of Non-Cyclic Photo-phosphorylation

 Chlorophyll absorbs light energy from the sun

 This light energy is then transferred to electron carriers (NADP & ADP).
 The energy from the electron carriers is used to drive the synthesis of ATP (the
universal energy currency).
 During photo-phosphorylation, ATP is generated through a process called
chemiosmosis (The process by which the movement of hydrogen ions across a
biological membrane generates ATP)
 The movement of protons across the membrane generates a gradient of protons, which
is used to power the synthesis of ATP.
 NADP is also reduced into NADPH during the process of photo phosphorylation.
This reduction of NADP means that it gains electron and hydrogen ions.
 The Reduction of NADP is an important step in the process of photosynthesis as it
aids in the production of energy-rich molecules that are needed to power cellular
processes.
 Oxygen is released into the atmosphere as it is a by-product of photosynthesis

Differences between Cyclic and Non-Cyclic Photo-Phosphorylation

 Cyclic Photo-phosphorylation
o Only Photosystem is involved
o P700 (photosystem 1) is the active reaction centre
o Electrons travel in a cyclic manner
o Electrons cycle to photosystem I
o ATP molecules are produced
o Water is not required
o NADPH is not synthesized
o Oxygen is not evolved as the by-product
o This process is predominant only in bacteria
 Non-Cyclic Photo-Phosphorylation
o Both Photosystem I and II are involved
 o P680 is the active reaction centre
o Electrons travel in a non-cyclic manner
o Electrons from Photosystem I are accepted by NADP
o Both NADPH and ATP molecules are produced
o Photolysis of water is present
o NADPH is synthesized
o Oxygen is evolved as a by-product
o This process is predominant in all green plants.

NOTE

 In Non-Cyclic Photo-phosphorylation, both Photosystems I and II are involved in the

electron transport chain. When photons of light are absorbed by PSII, they excite
electrons from water molecules, which are then passed through a series of electron
carriers, generating a proton gradient and reducing power in the form of NADPH.
During this process, ATP is also generated through chemiosmosis driven by the
proton gradient.
 In Cyclic Photo-phosphorylation, only Photosystem I is involved in the electron
transport chain. When photons of light are absorbed by photosystem I, they excite
electrons that are passed through a series of electron carriers, generating a proton
gradient that drives ATP synthesis by ATP synthase.
 Both non-cyclic and cyclic photophosphorylation can occur simultaneously in the
light-dependent stage of photosynthesis, generating both ATP and NADPH. The ATP
and NADPH produced during the light-dependent stage are then used in the light-
independent stage, also known as the Calvin Cycle, to synthesize organic molecules.

The Light Dependent Stage

 A photosystem is defined as the pigments in the chloroplast that are arranged into
light-harvesting complexes that are arranged around a reaction center. There are two
types of photosystems:
o Photosystem I (PSI) - 700 nm
o Photosystem II (PSII) - 600 nm
 The Light Dependent Stage takes place in the thylakoid membranes of the grana in the
chloroplast.
Light Dependent Reaction Diagram
Stages of the Light Dependent Stage

 Light causes the photolysis of H2O (the splitting of a water molecule) into; (i.e., H2O
1
 O2 + 2e- + 2H+)
2
o 2H+ ions
o 2e-
1
o O2
2

 The O2 is now either;

- Used in Respiration
- Diffused out of the leaf via the stomata

 The H+ ions are then picked up by NADP to form NADPH to be used in the light
independent reactions.
 Light energy that is absorbed by the chlorophyll causes;

- The 2e- to become excited, causing them to rise in energy level causing them
to leave the chlorophyll.
- The chlorophyll is ionized after the electrons leave

 The excited electrons are picked up by proteins in the chloroplast and passed along an
electron transport chain (ETC).
 Energy is released as the electrons move along the ETC. The energy is used to
actively transport/move protons from the stroma into the thylakoid space.

- The electrons now have a lower energy level when it reaches PSI. The
absorption of light by PSI re-energises the electron hence causing it to move
through another ETC.
- From here the electrons travel to NADP causing it to become NADPH
(reduced NADP). This reaction is catalysed by NADP reductase (an enzyme)
that is on the outer surface of the thylakoid membrane.

- The electrons can take two pathways when causing the reduction of NADP:
 Cyclic Phosphorylation - Where electrons travel from PSI and return to
PSI instead of reaching to NADP.
 Non-Cyclic Phosphorylation - Where electrons travel from PSII to PSI
and then to NADP.
- The Electrons cannot keep leaving PSII so more electrons are required. These
additional electrons come from photolysis.
- Photolysis provides electrons to PSII and Protons to the thylakoid space.

 This causes an electrochemical gradient to be formed causing it to now have a high

concentration of protons inside the thylakoid space.
  The only protein that protons (H+ ions) can diffuse through is an enzyme known as
ATP synthase.
 As protons are diffusing through ATP synthase it changes the shape of the protein.
o This change in the shape causes the energy to be transferred hence catalyzing
the reaction between ADP and the inorganic phosphate to form ATP.
o This reaction is known as Phosphorylation
 When the protons move back down the electrochemical gradient into the stroma.
Some of these protons are:
o Cycled and pumped back around to be used again
o Some of the protons are picked up by the co-enzyme NADP to form NADPH
(reduced NADP).

The Calvin Cycle (The Light Independent Stage)

 Takes place in the stroma of the Chloroplast

 Takes ATP, NADPH (reduced NADP) from the light-dependent stage and combines it
with CO2 to form glucose (G3P).
The Calvin cycle involves the light-independent fixation of carbon dioxide in the stroma of
chloroplasts. The essential stages of the Calvin cycle include:

 Carbon dioxide fixation:

o Carbon Dioxide (CO2) is added to a 5-carbon molecule called (RuBP)
ribulose bisphosphate. This addition is catalysed (sped up) by Rubisco
(Ribulose-1,5,-bisphosphate carboxylase)
o This forms an unstable 6-Carbon molecule.
o The 6C molecule breaks down into two 3-Carbon compounds known as
glycerate-3-phosphate (G3P) / (GP) / phosphoglyceric acid (PGA)
 Reduction:
o ATP and NADPH that were produced from the light dependent stage is used
for the conversion of G3P into glyceraldehyde-3-phosphate (GALP) / triose
phosphate (TP).
o Some of the TP is converted into organic molecules (such as; glucose) but
some will be used to regenerate RuBP.
o For every 6 molecules of TP:
 1 TP is used for glucose synthesis
 5 will be used for RuBP regeneration.
 Regeneration of RuBP:
o Using the energy generated from the hydrolysis of ATP into ADP, the TP is
converted back into RuBP.
o The cycle is completed and another round of carbon fixation can now take
place.
o Some of the G3P produced is used to regenerate RuBP, which is necessary for
continued carbon dioxide fixation.
  Carbohydrate synthesis:
o The remaining G3P molecules can be used to synthesize glucose and other
carbohydrates.
o GP and TP are used to make all biological molecules that the plants require to
grow.
 Glucose
 Made by the addition of 2 TP (triose phosphate) molecules
together
 The glucose can then be used to build polysaccharides (starch
& cellulose)
 Amino Acids
 Made from GP (glycerate-3-phosphate)
 Glycerol
 Made from GALP (glyceraldehyde-3-phosphate)
 Fatty Acids are made from GP
 Triglycerides are then formed by joining ester bonds and fatty
acids.

Overall, the Calvin cycle involves a series of enzyme-catalysed reactions that result in the
conversion of carbon dioxide into organic compounds that can be used by the plant for
energy and growth. ATP and NADPH, produced during the light-dependent reactions, are
essential for powering these reactions.
Limiting Factors

 A limiting factor is any environmental factor that prevents the increasing of the rate of
a reaction.

Limiting Factors that Affect Photosynthesis

 Light Intensity - An increase in the intensity of light increases the rate of reaction

 Concentration of CO2 (g)

- As the concentration of CO2 increases the rate of reaction also increases.

- Concentrations of 0.4% CO2 can maximise photosynthesis. However
concentrations that are above 0.4% can cause stomatal closure and a reduction
in photosynthesis.
  Temperature

- Temperatures around 25 degrees Celsius allow the photosynthetic enzymes to

work quickly.
- As temperature increases the rate of photosynthesis also increases
- However, as the temperature passes its optimum point the rate of reaction
decreases. At high temperatures the stomata will close to conserve water,
hence this stops gas exchange causing the rate of photosynthesis to be
reduced.

Uses of Limiting Factors

Limiting Factors can be Controlled to Maintain plant growth

Some ways that limiting factors can be used to improve plant productivity are:

 Controlled Light Intensity

- Artificial Light
- Shading the plants from direct sunlight
 Controlled Temperatures
- Heaters
- Ventilation
 Carbon Dioxide Concentration
- Enriching the CO2 concentrations by burning hydrocarbons (eg. propane)
 Supplying Water directly to the roots
- Sprinklers
 Supplying Mineral Nutrients directly to the roots
- Applying a specific number / amount of fertilizer to the different stages of the plant.
In The Caribbean

Growers use plastic and mesh greenhouses to control the conditions. For Example;

 Plastic to protect against heavy rain

 Mesh to reduce the intensity of the light
 Drip Irrigation is also used to water the plants (it reduces the cost of watering since
the water goes directly to the plants).
Biology (Unit 2) – Energy and Respiration (2.1– 2.10)
- Respiration
- Glycolysis
- The Mitochondrion, Link Reaction and Krebs Cycle
- Oxidative Phosphorylation
- Anaerobic Respiration in Mammals and Yeast
- Respiration Summary

Respiration
Cellular respiration is the transfer of chemical energy from organic molecule (Glucose) so
that it is available for cells in a usable form (ATP).
The organic molecules (carbohydrates, proteins and fats) are oxidised in order to make the
energy available for ATP synthesis.
- Carbohydrates - Short Term store of energy
- Fats - Long Term store of energy
- Protein - May be used as a source of energy if present in larger quantities that are
required for growth, repair and replacement.
Respiration:
- Takes place in the cytoplasm and mitochondria of cells
- There are two types of respiration:
o Aerobic Respiration - https://www.youtube.com/watch?v=eJ9Zjc-
jdys&t=36s&ab_channel=AmoebaSisters
o Anaerobic Respiration
Aerobic Respiration: Requires Oxygen - Occurs in the cytoplasm and Mitochondria of Cells.
Contains a few processes (Glycolysis, Link Reaction, Krebs Cycle, Electron Transport Chain,
Chemiosmosis)
- Glycolysis: The process begins in the cytoplasm with the breakdown of glucose into
two molecules of pyruvate. This process generates a small amount of ATP and
NADH.
Stages of Glycolysis – Involved in both aerobic and anaerobic respiration as this stage does
not require oxygen. Produces pyruvate and 2 ATP molecules
- ATP is hydrolysed into ADP and an inorganic phosphate
- Glucose is phosphorylated into fructose-1,6-bisphosphate by the addition of the
phosphate groups from 2 ATP molecules.
- Fructose-1,6-bisphosphate is an unstable molecule that immediately breaks down into
2 three carbon molecules (Triose Phosphate) (TP) also known as glyceraldehyde-3-
phosphate (G3P).
- 2 Hydrogen atoms and 2 electrons are removed from TP and are transferred to a
coenzyme called NAD to form NADH (reduced NAD).
- The removal of hydrogen from TP oxidises it and converts it into pyruvate
- The oxidation of TP generates 2 ATP molecules
Stages of the Link Reaction – Occurs in the matrix of the mitochondria, Produces CO2 and
NADH
- A carbon atom is removed from Pyruvate to form CO2 (Carbon Dioxide).
- Pyruvate is now converted into a 2-Carbon molecule called Acetate.
- Hydrogen is also removed from Pyruvate when converted into Acetate.
- The hydrogen is picked up by the coenzyme NAD to form NADH (reduced NAD).
- The acetate is combined with coenzyme A (CoA) to form Acetyl CoA.
Since one glucose molecule is converted into 2 pyruvates, the link reaction happens twice for
every glucose molecule. Hence, each molecule of glucose produces 2 molecules of Acetyl
CoA, 2 molecules of CO2 and 2 molecules of NADH.
The Krebs Cycle (The Citric Acid Cycle) – Occurs in the Mitochondria
Stages of the Krebs Cycle
- Acetyl CoA from the link reaction reacts with a 4-Carbon molecule (Oxaloacetate)
- The CoA portion of acetyl CoA is removed and returns to the link reaction to be
reused.
- This removal produces a 6-Carbon molecule called citrate
- Carbon & Hydrogen are removed from citrate to form CO2 (Carbon Dioxide) and
NADH (reduced NAD).
- The citrate is converted into a 5-Carbon compound
- The 5-Carbon compounds are converted into the 4-Carbon molecule (oxaloacetate)
via decarboxylation and dehydrogenation.
- ATP, 2 molecules of NADH (reduced NAD), one molecule of FAD and carbon
dioxide are also formed in this step.
- This cycle takes place twice for each glucose molecule that is respired aerobically

Oxidative Phosphorylation – Takes place across the inner mitochondrial membrane and
involves the electron transport chain and chemiosmosis
 - The coenzymes NADH (reduced NAD) and FADH (reduced FAD) release hydrogen
atoms which split into hydrogen ions and electrons.
- The electrons are passed onto electron carriers which are embedded within the inner
mitochondrial membrane and travel along a series of electron carriers known as the
electron transport chain.
- As the electrons travel between the electron carriers, they lose energy. This energy is
used by the carriers to pump hydrogen ions from the mitochondrial matrix across the
inner membrane.
- Hydrogen ions accumulate in the intermembrane space and this generates a proton
gradient (an electrochemical gradient) across the membrane
- Hydrogen ions then flow back into the matrix through the enzyme (ATP synthase)
which uses the movement of the hydrogen ions to add a phosphate group onto ADP to
form ATP. This process is known as chemiosmosis.
- Once the electrons reach the end of the electron transport chain, they are passed onto
oxygen (the final electron acceptor).
- Oxygen combines with electrons and hydrogen ions to form water (one of the
products of aerobic respiration).
Total ATP Production
Aerobic respiration produces a total of 38 ATP molecules for each molecule of glucose
respired.
- Glycolysis: direct production of 2 ATP
- Glycolysis: 2 NADH (reduced NAD) are converted into 6 ATP (2 x 3) in oxidative
phosphorylation
- Link reaction: 2 NADH (reduced NAD) are converted into 6 ATP (2 x 3) in oxidative
phosphorylation
- Krebs cycle: direct production of 2 ATP
- Krebs cycle: 6 NADH (reduced NAD) are converted into 18 ATP (6 x 3) in oxidative
phosphorylation
- Krebs cycle: 2 FADH (reduced FAD) are converted into 4 ATP (2 x 2) in oxidative
phosphorylation
Total ATP = 2 + 6 + 6 + 2 + 18 + 4 = 38 ATP
The Mitochondrion
The mitochondrion is the organelle in which the rest of respiration occurs. This is the site of
ATP production during aerobic respiration. It is self-replicating so can become numerous in
cells with high energy requirements. It contains a double membrane with folds called cristae,
which provides a large surface area for respiration.
Mitochondria are membrane-bound organelles found in most eukaryotic cells. They are
often called the "powerhouses" of the cell because they produce ATP, the main source
of energy for the cell. The structure of the mitochondrion is well-suited to its function
of producing energy.
The mitochondrion has two membranes: an outer membrane and an inner membrane
that is highly folded into structures called cristae. The space between the two
membranes is called the intermembrane space, while the space inside the inner
membrane is called the matrix. The cristae provide a large surface area for ATP
synthesis to occur, while the inner membrane is impermeable to most substances,
allowing for the generation of a proton gradient that drives ATP synthesis.
The inner membrane contains several protein complexes, including the electron
transport chain, which is responsible for generating the proton gradient that drives ATP
synthesis. The matrix contains enzymes involved in the citric acid cycle (also known as
the Krebs cycle), which generates the electron carriers NADH and FADH2 that feed
into the electron transport chain.
Mitochondria are;
- Rod-shaped organelles 0.5 – 1.0 µm in diameter
- They are the site of aerobic respiration in eukaryotic cells
- The function of mitochondria is to synthesize ATP
- Synthesis of ATP in the mitochondria occurs during the last stage of respiration called
oxidative phosphorylation.

Structures of the Mitochondria

 - Mitochondria have two phospholipid membranes
o The outer membrane (Smooth & Permeable to several small molecules)
o The Inner membrane (Folded (cristae), Less permeable, The site of the
electron transport chain (used in oxidative phosphorylation), Location of ATP
synthase (used in oxidative phosphorylation)
- The intermembrane space:
o Has a low pH due to the high concentration of protons
o The concentration gradient across the inner membrane is formed during
oxidative phosphorylation and is essential for ATP synthesis
- The matrix:
o Is an aqueous solution within the inner membranes of the mitochondrion
o Contains ribosomes, enzymes and circular mitochondrial DNA necessary for
mitochondria to function

STRUCTRES AND FUNCTIONS OF THE MITOCHONDRIA

Structure Composition Function
Outer Membrane - Phospholipid Bilayer Permeable to:
- Proteins - Pyruvate
- Oxygen
- Carbon Dioxide
- ATP
- ADP
- Not Glucose
Inner Membrane - Phospholipid Bilayer with - Pumps protons into
protein complexes of intermembrane space
electron transport chain - Making ATP permeable to
and ATP synthetase the same molecules that the
outer membrane is
permeable to with the
exception of hydrogen ions
and glucose
Intermembrane space - Lower pH than Cytosol - Site of high concentration
- Matrix of protons
Matrix - Protein rich region - Link Reaction
- Contains DNA loop - Krebs Cycle
- Ribosomes - Production of Urea
- Many enzyme molecules
DNA - Loop of double stranded - Codes for 13 of the
DNA (not combined with proteins used in the
histone proteins) mitochondrion; genes are
transcribed as mRNA
- The rest of the
mitochondrial proteins are
coded for by DNA in the
nucleus
70s Ribosomes - rRNA & Proteins Translation – Assembly of
Amino acids to form
 proteins

ANAEROBIC RESPIRATION
Anaerobic Respiration Equation;
C6H12O6  CH3CH(OH)COOH
Glucose  Lactic Acid
This is the respiration in the absence of oxygen. In mammals, glucose can be converted into
lactate (lactic acid) which release small amounts of energy in the form of ATP.
Anaerobic respiration occurs in the cytoplasm when there is not enough oxygen to be
absorbed for aerobic respiration to provide energy. Muscle tissues respire anaerobically when
there is not enough oxygen to produce energy.

Stages of Anaerobic Respiration

- (Glycolysis) Glucose is converted into 2 pyruvates with the net release of 2 ATP
molecules and 2 NADH molecules.
- NADH is added to pyruvate to produce lactate and NAD. This regenerates more
oxidised NAD for glycolysis.
This enables respiration to continue and ensures that small amounts of energy can still be
made in the absence of oxygen, allowing biological reactions to keep repeating.
Continued anaerobic respiration results in the build-up of lactate (lactic acid), which
needs to be broken down.
Cells can convert lactate back into pyruvate, which is then able to enter aerobic
respiration at the Krebs Cycle.
Anaerobic Respiration and Muscles
Anaerobic respiration in muscle tissues is useful as it provides energy as ATP very quickly to
support exercise. However, the build up of lactic acid in muscle tissues lowers the pH and
reduces the efficiency of enzyme causing the body to feel tired.
After exercise during the recovery period, oxygen uptake remains high as oxygen is required
for;
- Aerobic respiration of lactic acid in the liver (The liver cells have the ability to
convert lactic acid into glucose)
- Re-oxygenating haemoglobin in the blood
- RE-Oxygenating myoglobin (store of oxygen in muscle tissue)
- Resynthesis of ATP and creatine phosphate in muscle tissue
- Supporting high rates of respiration in all organs after exercise

Anaerobic Respiration can be used in bread making, brewing of alcohols and wine making
via the Fermentation process in yeast

Equation for the anaerobic respiration of yeast; C6H12O6  2C2H5OH + 2CO2

Comparison of Aerobic and Anaerobic Respiration

Oxygen Debt
At the end of exercise an oxygen debt will be built up. This is why humans and animals
continue to breathe deeply after taking a short burst of strenuous exercise.
Lactate dehydrogenase catalyses the reaction in which lactate is converted into pyruvate. This
happens in the liver. Some pyruvate is converted to glucose by the reverse of the reactions of
glycolysis. This requires energy which is provided by the oxidation of pyruvate in
Mitochondria.
After the exercise is over, the body must continue to metabolize these by-products, which
requires oxygen. This extra oxygen consumption is known as the oxygen debt. The body
repays this debt by continuing to consume oxygen even after the exercise has stopped, until it
has fully metabolized the accumulated by-products.

Advantages of Oxygen Debt:

- Allows the body to continue to produce ATP (energy) even in the absence of
sufficient oxygen.
- Enables individuals to engage in short bursts of high-intensity exercise without
immediately becoming fatigued.
- Can improve overall fitness levels over time as the body becomes more efficient at
metabolizing by-products and recovering from exercise.
Disadvantages of Oxygen Debt:
- Can lead to muscle fatigue and soreness, as well as a build-up of lactic acid and other
metabolic by-products.
- May result in decreased performance during prolonged exercise, as the body is unable
to sustain the same level of intensity without sufficient oxygen.
- Can increase the risk of injury or overtraining if individuals do not allow sufficient
time for recovery and replenishment of oxygen stores.
 ENERGY AND NUTRIENT FLOW
An Ecosystem - is defined as a community of living organisms, along their physical and
chemical environment.
A Habitat - is defined as a place where an organism lives. A habitat should include physical
and biological factors that organisms need to survive and reproduce, such as; food, water,
shelter and other resources.
An Ecological niche - refers to the role or position that an organism occupies within an
ecosystem. An ecological niche includes both physical and biological resources that an
organism has with other species.
A Trophic level - is defined as the position that an organism occupies in a food chain or food
web. The trophic level describes the organism’s source of energy and the way it interacts with
other organisms in the ecosystem. Primary producers occupy the first trophic level followed
by Primary consumers, Secondary consumers and so on depending on the complexity of the
food web.

Energy Flow of Energy

Organisms gain food from an energy source / sources and provided energy for other
organisms that eat them. The relationship between an energy source and organisms are
represented by a food chain. Each organism occupies a trophic level

- Producer – Organisms which produce biomass by capturing the energy from sunlight
are called producers. An autotrophic organism that uses either light energy or energy
from simple chemical reactions to fix carbon dioxide and produce biological
molecules.
- Consumer – An organism that obtains energy in organic compounds, usually feeding
on living organisms, there are several consumer trophic levels including decomposers
(organisms that obtain energy by breaking down compounds in dead and decaying
organisms)
o Primary Consumer - An organism which feeds on a producer is called primary
consumers and will also be herbivores, since producers tend to be mostly
green plants.
o Secondary Consumer - The next organism in the food chain is the secondary
consumer which will be eaten by the tertiary consumer.
Producers are eaten by more than one consumer. Many consumers feed on more than one
type of food organism. There are many food chains within an ecosystem. A food web gives a
better indication of all these different feeding relationships.
A food web show some of the complexity of feeding relationships in an ecosystem. They
can’t show all of the relationships as it will be too complex.
Both the food chain & food web show energy flow between trophic levels. The arrows do not
indicate how much energy flows.
Example of Food Chain:

Decomposers are also part of food webs. They break down dead material and allow nutrients
to be recycled.
Decomposers are microorganism such as bacteria and fungi are able to feed off and
decompose dead organic matter. They do this by secreting digestive enzymes onto the
organism. They digest the tissues of the dead organisms into smaller molecules, such as
glucose which is absorbed externally by a process known as saprotrophic nutrition
(organisms that do this are called saprobionts). Decomposers play an important role in
breaking down waste products and enabling the chemical elements to be recycled.
Fungi form symbiotic relationships with plant roots. Fungi consist of long, thin strands called
hyphae which connect to plant roots to form structures called mycorrhizae. This increases the
surface area of the soil that the plant can obtain mineral ions from. This enables the plant to
access more minerals and the fungi receives glucose (and other organic compounds) in return.

Respiration is not 100% efficient at energy transferring energy from food to ATP. During
respiration, much of the energy is transferred as heat to the surroundings. Eventually all the
energy that entered the ecosystem leaves as infrared radiation to the surroundings and is
radiated away from the Earth into space.
 ECOLOGICAL PYRAMIDS & EFFICIENCY
Ecological Pyramids are pyramids that illustrate the amount of energy contained in
the biomass (the total mass of living material) of organisms at each trophic level. The
length of each box represents the quantity of energy present.

Ecological Pyramids should be;

- Drawn to scale, so that each bar is proportional in size to the amount of energy it
represents
- The Pyramids are always the widest at the base (This is due to the large amount of
energy that are contained in the biomass of the producers) and decrease in size as they
go up due to the decrease in energy level.
- The levels of a pyramid of energy should be labelled; Producer, primary consumer,
secondary consumer…and so on.
- The units kJ m-2year-1 (energy, per unit area, per year) should be used
- The higher you move up the pyramid / the higher you move up at each trophic level,
the more energy decreases. This is due to only about 10% of the energy is passed on
- At each trophic level energy is lost due to; incomplete consumption, incomplete
digestion, loss of heat energy during respiration and loss of energy due to excretion of
waste products (CO2, Water, Urea)
Example of an Ecological Pyramid

Note: Ecological Pyramids do not show microorganisms that are important, such as
decomposers and parasites.

The efficiency of energy flow between trophic levels is calculated by:

Ecological Efficiency =
energy available ¿ atrophic level ¿ x 100
energy consumed by previous trophic level
When a consumer ingests another organism not all the chemical energy in the consumer’s
food is transferred to the consumer’s tissues.
- Only about 10% of the energy is available for the consumer to store in their tissues
- 90% of the energy is lost in the environment
o Not every part of the food organism is eaten hence energy is lost to the
environment.
o Consumers are not able to digest all of the food they ingest (e.g., cellulose in
plants, fur of animals). The undigested foods are egested as faeces. The
chemical energy of the undigested food is lost to the environment.
o Energy is lost to the environment via respiration and heat produced by the
organism
 THE NITROGEN CYCLE
The nitrogen cycle is defined as the process that converts nitrogen in the air to nitrate in the
soil. Nitrogen is important for several reasons:
- Building block of life: Nitrogen is a key element in the building blocks of life, such as
amino acids, proteins, and nucleic acids like DNA.
- Essential for plant growth: Plants need nitrogen to grow, and nitrogen is often the
limiting factor in plant growth. Nitrogen is a key component of chlorophyll, which is
necessary for photosynthesis.
- Food production: Nitrogen is a crucial component in the production of fertilizers,
which are used to increase crop yields and food production.
- Atmospheric balance: Nitrogen makes up about 78% of the Earth's atmosphere and is
essential for maintaining the atmospheric balance. It helps to regulate the temperature
and composition of the atmosphere.

Environmental benefits: Nitrogen is important for maintaining healthy ecosystems. Nitrogen

fixation, which is the process of converting atmospheric nitrogen into a usable form for
plants, is carried out by certain bacteria and helps to enrich the soil.
The nitrogen cycle can be broken down into several key stages:
- Nitrogen fixation: Nitrogen gas (N2) is converted into ammonium (NH4+) by
nitrogen-fixing bacteria in the soil or in the roots of leguminous plants.
- Nitrification: Ammonium is converted into nitrite (NO2-) and then nitrate (NO3-) by
nitrifying bacteria in the soil.
- Assimilation: Plants take up nitrate from the soil and use it to build amino acids,
nucleic acids, and other nitrogen-containing organic molecules.
- Ammonification: decomposers break down organic matter, such as dead plants and
animals, releasing ammonium back into the soil.
- Denitrification: denitrifying bacteria convert nitrate back into nitrogen gas, which is
released back into the atmosphere.
These stages work together to create a cycle that constantly recycles nitrogen through the
environment, making it available to plants and other organisms.
Nitrification – The conversion of ammonia to nitrate ions
1. Oxidation of Ammonium Ions to Nitrite Ions via Nitrosomonas (nitrifying bacteria)
2NH3 + 3O2  2NO2- + 2H+ + 2H2O
ammonia + oxygen  nitrite ions + hydrogen ions + water
2. Oxidation of Nitrite ions to nitrate ions via Nitrobacter
2NO2- + O2  2NO3-
Nitrite ions + oxygen  nitrate ions
 ECOSYSTEMS
Organisms interact with other organisms in an ecosystem.
Abiotic Factor – Any aspect of non-living components of an ecosystem such as; temperature,
water availability, light, soil nutrients, and pH levels.
Biotic Factor – Living components of an ecosystem such as; plants, animals, fungi and
microorganisms that interact with eachother and their environment.
The types of interactions between organisms are examples of biotic factors:
- Competition
- Cooperation with organisms
- Predation
- Disease

1. Competition – There is competition with other species for resources, such as space,
water, energy and nutrients. This can either be:
- Interspecific Competition – Competition between different species
- Intraspecific Competition – Competition between members of the same species
Competitive Exclusion describes the competition between two or more species for the same
limited resources in a specific environment.
- The principle states that when two species with similar ecological niches compete for
the same resources, one species will eventually outcompete and displace the other,
leading to the extinction or local extinction of the weaker species.
- This occurs because the successful species is better adapted to the environmental
conditions and is able to utilize the resources more efficiently, giving it a competitive
advantage.
- Competitive exclusion is an important concept in ecology and has implications for
conservation biology and the management of natural resources.
Resource Partitioning refers to the process by which different species reduce competition for
limited resources in order to coexist within an ecosystem.
- This can occur in several ways, such as through the use of different food sources,
utilization of different habitats or niches, or through differences in feeding behaviour
or timing.
- Resource partitioning is a key concept in ecology and is important for understanding
how species can coexist and maintain biodiversity within an ecosystem.

2. Cooperation refers to a form of symbiosis in which two or more species work

together to benefit each other, or achieve a common goal.
- This type of interaction is commonly referred to as mutualism, and it is characterized
by a positive impact on the fitness and survival of both species involved.
- An example of cooperation in an ecosystem could be the mutualistic relationship
between pollinators such as bees and flowering plants, where the bees obtain food in
 the form of nectar and pollen, while the plants benefit from the pollination services
provided by the bees, which enable them to reproduce.

3. Predation refers to the interaction between two organisms, where one organism,
known as the predator, hunts, kills, and eats another organism, known as the prey.
- Predation is an important ecological process that helps to regulate population sizes,
maintain species diversity, and shape community structures.
- Predators have evolved a range of adaptations, such as sharp teeth and claws, keen
senses, and stealthy movements, to capture and consume their prey, while prey have
also evolved various defences mechanisms, such as camouflage, toxins, and warning
signals, to avoid being eaten.

4. Disease defined as a disturbance or abnormality in the functioning of an organism's

body that results in a loss of its normal physiological or behavioural activities.
- Diseases can be caused by a variety of factors, such as pathogens (e.g., viruses,
bacteria, fungi), genetic mutations, environmental stressors, or lifestyle choices.
- Diseases can have significant impacts on the ecosystem, as they can affect the
population dynamics of species, alter nutrient cycling, and disrupt food webs.
- Disease can also play a role in natural selection, as individuals with genetic or
behavioural adaptations that allow them to resist or tolerate diseases are more likely to
survive and reproduce.
 BIODIVERSITY
Biodiversity is defined as the variety of living organisms present in a given ecosystem or on
Earth as a whole. This includes the diversity of species, their genetic variation within
populations, and the range of different ecosystems and biomes that exist.
Biodiversity of an area is a measure of the:
- Different Ecosystem
- Number of Species
- Number of Individuals of each species
- Genetic Variation within each species present in an area

Ecosystem Diversity - refers to the variety of ecosystems or habitats in a particular region or

on a global scale.
- It encompasses the different biotic and abiotic factors that make up the various
ecosystems, including the organisms that inhabit them, the physical and chemical
characteristics of the environment, and the interactions between them.
- Ecological diversity is important as it provides opportunities for species diversity.

Species Diversity - refers to the variety of different species that exist within a particular
ecosystem or geographical area.
- This can include the number of different species present, as well as their relative
abundance and distribution.
- Species diversity helps to measure the health and stability of ecosystems.
- High species diversity generally means that there are a range of different organisms
that are able to thrive within the ecosystem.

Genetic Diversity - refers to the variation of genes within a population, species, or ecosystem.
- It is a measure of the genetic differences that exist among individuals within a
population or among populations of the same species.
- Genetic diversity is important for the survival of a species, as it allows individuals to
adapt to changing environmental conditions and provides a pool of genetic resources
that can be used for future evolution.
- Factors that contribute to genetic diversity include mutations, genetic drift, gene flow,
and natural selection.
 Maintaining Biodiversity
Conservation – is defined as the protection, management, and restoration of
ecosystems, species, and habitats that are threatened or endangered. Conservation
biology is a field of study that focuses on the preservation of biodiversity, which is the
variety of life on Earth.

Reasons to maintain biodiversity:

- Biodiversity contributes to the stability and resilience of ecosystems by providing a
variety of ecological niches and services that support the functioning of ecosystems.
- Biodiversity is essential for the provision of ecosystem services such as nutrient
cycling, water purification, soil formation, and climate regulation.
- Biodiversity provides genetic resources for crop improvement, medicine
development, and other important applications.
- Biodiversity provides opportunities for scientific research and discovery, leading to
new insights and innovations.
- Biodiversity has aesthetic, cultural, and recreational values, providing a sense of
identity and well-being for human communities.
- Biodiversity is important for the survival and adaptation of species, as it provides a
pool of genetic resources that can be used for future evolution and adaptation to
changing environmental conditions.
- Biodiversity is an indicator of the health and sustainability of ecosystems and is a
critical component of sustainable development.

In Situ Conservation (Natural Habitat Conservation)

The best way to conserve any species is to keep them in their natural habitat.

In situ conservation can involve:

- Establishing protected areas such as; national parks, wildlife reserves, protected
marine areas, to safeguard ecosystems and habitats.
- The restoration and management of degraded ecosystems such as; wetlands, forests
and grasslands to enhance their ecological functions and services.
- Preventing invasive species from being introduced to the protected habitat
- Reclaiming ecosystems that have been damaged by human activities

Ex Situ Conservation (Outside of their Natural Habitat)

Involves the preservation of species and genetic diversity outside of their natural
habitats.

Ex Situ conservation can involve:

- Captive breeding programmes
- Creating Botanical Gardens that serve as living museums of biodiversity to preserve
the plants
- Captivity of animals (placing them in zoos as a form of both entertainment and
preservation)
Examples of Ex Situ Conservation includes;
Zoos - are used as a form of entertainment and also as a form of ex situ conservation.
Some functions of zoos are:
- For Protecting endangered and vulnerable species
- For breeding programmes for species that will breed in captivity
- Research of species to gain a better understanding of their breeding habits, habitat
requirements and genetic diversity

Sperm Banks – Different zoos cooperate with eachother to create genetic diversity and so
that species do not become inbred.
The process involves:
- Collect semen from suitable males
- Test the sperm for motility (the ability of an organism or a cell to move or exhibit
movement)
- Dilute with a medium containing buffer and albumen (a plasma protein)
- Put small volumes into thin tubes known as straws
- Store the sperm samples in liquid nitrogen at -196˚C
- The sperm samples are then thawed and used for artificial insemination

Young animals of over 30 different species, including Rhinoceros, cheetahs have been
produced using sperm from sperm banks.

Seed Banks – Seeds are collected from plants in the wild and put into long-term storage.

The seeds are stored by:

- Dehydrating them so there is only 5% water in the seed (by doing this it slows down
the seed’s metabolism and makes it remain viable for many years)
- Storing them at -20˚C
 Transport in Plants
Transport Systems are needed to provide water for photosynthesis and to get rid of waste
substances. Plants can’t obtain these things by simple diffusion as they are multicellular
organisms and have a large surface area to volume ratio. Diffusion would take place too
slowly so plants have transport systems.

Vascular Bundle

The vascular bundle contains Xylem & Phloem vessels which transport water and sugars
from one part of the plant to another. The vascular bundle is found within the plant stem, with
the xylem vessels right on the inside and the phloem tissue at the middle of the vascular
bundle.

- Xylem Vessels
 Transport water and mineral ions from the roots to the rest of the plant
 Made up of dead, hollow cells with no end cell walls. This means that one
continuous tube is formed when xylem cells are stacked on top of eachother.
 The cell wall contains lignin (a tough, woody substance) that provides support
to the structure and to the plant.
 The xylem cells have no organelles or cytoplasm. This creates more space
inside the vessel for transporting water.
 - Phloem Vessels
 Transport dissolved substances such as: sucrose, amino acids from sources
(where they are made) to sinks (where they are used).
 Leaves are sources as they produce glucose from photosynthesis
 Roots and bulbs (underground stem) are sinks
 Phloem vessels are made up of 2 types of cells: sieve tube elements and
companion cells.
 Sieve Tube Elements:
 Living cells that are joined end-to-end to form sieve tubes. At the end
of these sieve tubes are holes that allow solutes to move from one cell
to the next
 Contain little cell contents to reduce resistance to flow of phloem sap
 Sieve pores allow for the easy flow between sieve tube elements.
 Companion Cells
 Required for each sieve tube to survive, as it contains a nucleus and is
packed full of mitochondria that provides energy for the active loading
of sucrose into the sieve tube element
 Pumps proteins and co-transporter proteins in the cell surface
membranes for absorption of sucrose from the apoplast pathway from
mesophyll cells.

Translocation - The movement of phloem sap from a source to a sink. Here is the process:

- Sugar molecules are produced in the photosynthetic cells of the leaves, where they are
converted from the products of photosynthesis.
- The sugar molecules are actively transported into the phloem cells, where they move from
the source region (e.g., leaves) to the sink region (e.g., roots) of the plant.
- This movement of sugar molecules occurs through a process called pressure flow, where the
sugars are loaded into the phloem at the source region and unloaded at the sink region.
- The loading of sugar into the phloem cells at the source region causes a high concentration
of sugar in the phloem, which creates a water potential gradient that draws water into the
phloem cells through osmosis.
- The influx of water into the phloem cells increases the pressure within the phloem, which
pushes the sugar-rich sap toward the sink region of the plant.
- At the sink region, the sugar molecules are actively transported out of the phloem cells and
used by the plant for growth and energy production.

UPTAKE OF WATER & IONS

There are 4 ways to transporting water and ions in plants:

- Absorption from the soil

- Short distance movement of water and ions via roots, stems, leaves
- Long distance movement of xylem sap & phloem sap from the roots to leaves
- Evaporation and loss of water vapour from the leaves into the atmosphere

Plants have special adaptations that allow them to absorb ions and water from the soil. These
adaptations are:

- Long tap roots - Reach sources of water and ions that are deep in the soil
- Extensive, branching root systems - occupy a large volume of soil
- Epidermal Cells - contain root hairs that increases the surface area for absorption
- Thin root hairs - that can extend between soil particles
Absorption of Ions:

- Roots Hairs – Contain tiny root hairs that increase the surface area available for
absorption
- Active Transport – The ions are absorbed via active transport which requires energy
in the form of ATP
- High Concentration of Ions in soil – Faster absorption rate
- Selective absorption – Plants can absorb ions based on their needs. E.g., If they need
to grow, they will absorb more nitrogen ions.
- pH of the Soil – Some ions may be less available to plants in alkaline soil whilst
others are less available in acidic soils
- Fungi – Certain fungi can form a symbiotic relationship with plant roots and help
increase ion absorption

Absorption of Water:

- Root Hairs – Water enters the plant through root hairs

- Larger Surface area – Root hairs that cover a larger surface area allow for more water
to enter the plant
- Osmosis – The water moves through the cells of the root cortex via osmosis
- Xylem – The water moves up the plant’s stem via the xylem vessels. This is known as
a transpiration stream.
- Transpiration – When water evaporates from the plant, the cohesion of the water
molecules pulls more water from the soil up
- The stomata – Allows for water to be diffused out of the leaves of the plant
 Transpiration
The loss of water vapour through evaporation from a plant’s surface.
It mainly happens through gaps in the leaf called the stomata, which need to open during the
daytime to allow gas exchange. Plants need to take in carbon dioxide for photosynthesis and
get rid of oxygen, which happens through the stomata.
A side-effect of this is that water vapour can also diffuse out of the leaf through the stomata
this is known as transpiration.
Factors that affect the rate of transpiration are:
- Light Intensity – As light intensity increases, the rate of transpiration also increases
due to the plant photosynthesising more and more gas exchange is required for the
plant to absorb more CO2. The stomata open for a longer period of time on summer
days hence more water is lost.
- Temperature – As temperature increases, the rate of transpiration also increases. This
is due to the higher temperatures causing water molecules to diffuse faster out of the
stomata.
- Wind – As the wind speed increases, the rate of transpiration also increases. The wind
will immediately blow away any water molecules that have just diffuses out of the
leaf.
- Humidity - more humid conditions decreases the rate of transpiration. Humidity is a
measure of the level of moisture in the air. The more humid the air surrounding a leaf,
the lower the water potential gradient between the inside of the leaf and the outside.

Transpiration can cause water to be pulled up from the soil. Here are some ways in which this
can occur:
Cohesion-tension: Where water molecules stick together due to cohesive forces and are
pulled upwards by tension created by the evaporation of water from the leaves.
Transpiration stream: The movement of water and minerals from the roots to the leaves of a
plant through the xylem tissue. The mechanism of cohesion-tension drives the transpiration
stream.
Transpiration Pull: The negative force created by the evaporation of water from the leaves,
which pulls water molecules from the roots to the leaves through the xylem tissue.
Capillarity: The ability of water to climb up narrow tubes, such as the xylem tissue in plants,
due to the combination of adhesive and cohesive forces.
NOTE:
Cohesion:
- This refers to the attraction between water molecules, which causes them to stick
together and form a continuous chain or column of water.
- This cohesion is due to the hydrogen bonds between water molecules.
Adhesion:
- This refers to the attraction between water molecules and the inner walls of the xylem
tissue.
- The walls of the xylem are made of cellulose and other complex polysaccharides,
which have a slight positive charge that attracts the negatively charged water
molecules.
 CIRCULATORY SYSTEM OF MAMMALS
The circulatory system of mammals is a closed, double circulation system. This is because of
how the blood flows inside vessels in its journey around the body.
Blood