AQA A2 Biology Unit 4

Populations

Specification

Populations and ecosystems

A population is all the organisms of one species in a

habitat. Populations of

different species form a

community.

Within a habitat a species occupies a niche governed by adaptation to both biotic and

abiotic conditions.

Investigating populations

A critical appreciation of some of the ways in

which the numbers and distribution of organisms

may be investigated.

Random sampling with quadrats and counting

along transects to obtain quantitative data.

The use of percentage cover and frequency as

measures of abundance.

The use of mark–release–recapture for more mobile species.

Variation in population size

Population size may vary as a

result of

• the effect of abiotic factors

• interactions between

organisms: interspecific and

intraspecific competition and

predation.

Human populations

Population size and structure,

population growth rate, age-

population pyramids, survival

rates and life expectancy.

3.4.1 The dynamic equilibrium of populations is affected by a number of factors.Candidates should be able to:• carry out experimental and investigative activities, including appropriate risk management• consider ethical issues when carrying out fieldwork, chiefly those relating to the organisms involved and their environment• analyse and interpret data relating to the distribution of organisms, recognising correlations and causal relationships• appreciate the tentative nature of conclusions that may be drawn from such data.• interpret growth curves, survival curves and age-population pyramids• calculate population growth rates from data on birth rate and death rate.• relate changes in the size and structure of human populations to different stages in demographic transition.

Definitions• Abiotic: Ecological factor that makes up part of the non-biological environment• Biotic: Ecological factor that makes up part of the living environment• Ecosystem: More or less self contained functional unit in ecology made up of all

interacting biotic and abiotic factors in a specific area• Population: A group of individuals of the same species that occupy the same

habitat at the same time• Species: A group of similar organisms that can breed together to produce fertile

offspring• Community: The organisms of all species that live in the same area• Habitat: The place where an organism normally lives, which is characterised by

physical conditions and the species of other organisms present• Niche: All conditions and resources required for an organism to survive,

reproduce and maintain viable population• Intraspecific: Competition between organisms of the same species• Interspecific: Competition between organisms of different species• Predator: An organism which feeds of another organism known as the prey

1.1 Populations and Ecosystems

The environment can include abiotic and biotic factors such as temperature, light (abiotic), predation and competition (biotic)

The life supporting layer of land, air and water that surrounds the earth is known as the biosphere

• The ecosystem is made up of biotic and abiotic features

• There are two major processes to consider: • The flow of energy through the system• The cycling of elements within the system• There are a number of species in an ecosystem which

make up many groups of individuals that together make up a population

Ecosystems

1.2 Investigating PopulationsWhen studying a habitat the number of individuals in an individual space needs to be counted this is

the abundance

Only small samples are taken due to the time consuming nature

As long as samples are representative the conclusions will be valid

• Size of quadrat: Larger species need larger quadrats, if a species occurs in series of groups then a large number of small quadrats is used

• Number of samples: The larger the number the more reliable the results

• Position of quadrat: Statistically significant results are obtained by random sampling

Factors to consider when using quadrates:

• To avoid bias random sampling is used• 1. Lay out two long tape measures at right angles along two sides of

the study area• 2. Obtain series of coordinates by using random numbers taken

from a computer • 3. Place a quadrat at the intersection of each pair of coordinates

and record the species within it

Random Sampling

• A line transect can be used in which a string/tape is stretched across the ground and any organism that passes the line is recorded

• A belt transect is a strip marked using a second parallel line, species within the belt and between the lines are recorded

Systematic sampling along Transects

• Random sampling and counting along transects can obtain measures of abundance in several ways:

• Frequency: Likelihood of a particular species occurring in a quadrat. It gives quick idea of species present and general distribution within an area but doesn’t provide density or distribution of species

• Percentage Cover: Estimate of the area within a quadrat. Useful where species is particularly abundant, data can be collected rapidly bur it occurs in overlapping layers

• To obtain reliable results the sample size needs to be large and a mean needs to be collected

Measuring Abundance

• Due to animals being mobile this method is used • Once an animal is caught it is marked then released, later on more individuals are

captured and the number marked is recorded• The technique relies on assumptions:• Proportion of marked to unmarked individuals in the second sample is the same

as the proportion of marked to unmarked individuals in the population as a whole

• The marked individuals released from the first sample distribute themselves in sufficient time

• The population has a definite boundary so no immigration or emigration• There are few deaths and births• The marking is not toxic or makes the animal more liable to predation• The mark or label is not lost or rubbed off

Mark-release-recapture

• The first stage is to present data in a table or graph so data can be compared and then calculate standard deviation

• Correlation and causation can be analysed • Statistical tests can also be used to calculate strength and direction of any

correlation • Spearman rank, chi squared and standard error can be used

Analysing data

Population = Total number of individuals in the first sample X Individuals in the second sampleNumber of marked individuals recaptured

Type of Trap Method of Marking

Pitfall trap: Insects, Small Mammals Microchip

Electrofishing : Fish Paint or permanent marker onto animal

Cage set up with food in: Mice, Voles Photo showing unique markings

Removal method: blocks of part of environment so can collect fish

Visible implant or tag

Glue Trap: Rodents Toe Clippings: Vertebrates

Sweepnet moved through plants: Ground insects

Fur Removal

Wire funnel trap: Insects in tall vegetation

1.3 Variation in Population Size

Population Growth Curves

• 1. Period of slow growth as the initially small number of individuals reproduce to slowly build up their numbers

• 2. Period of rapid growth where the ever increasing number of individuals continue to reproduce. The population size doubles during each interval

• 3. Period when population growth declines until size becomes stable, the decline can be due to food shortage or predation

There are 3 phases:

1.

2.3.

Population Size• Mineral ions• Light• Temperature• Oxygen• Food

Population size depends on limiting factors:

• Temperature: Optimum temperature needed for best survival as otherwise enzymes work slower and metabolic rate is reduced due to denaturation

• Light: Ultimate source of energy, the stronger the light intensity the faster the rate of photosynthesis causing a faster growth of plants thus a larger population

• pH: Optimum pH needed otherwise enzymes don’t work to full potential as denatured

• Water/Humidity: In low water areas only species well adapted to dry conditions survive. The more humid an area the slower the rate of transpiration

Abiotic Factors

1.4 CompetitionIntraspeci

fic Competiti

on

• Between the same species• Compete for food, water, mates• Greater the resources availability the larger the population

Interspeci

fic Competiti

on

• Between different species• For food, light and water • If two species occupy in the same niche one will normally have a competitive

advantage • The population of the stronger species will gradually increase while the other

diminishes eventually to be removed: Competitive exclusion principle• No species can occupy the same niche indefinitely when resources are

limiting

Intraspecific Competition Interspecific Competition

1.5 Predation• Predators eat their prey, reducing prey population• The predators become in greater competition with

each other over the prey left• Predator population is reduced causing fewer prey to

be eaten• The prey population increases• Due to more prey the predator population then

increases

The relationship between prey and predator:

The fluctuations in population as also due to disease and

climatic factors not just predation

• The population then evolves to be better adapted to harsh conditions

Population crashes create selection pressure where

survival of the fittest occurs, the survivors will reproduce

1.6 Human Populations• The development of agriculture• The development of manufacturing and trade that created

industrial revolution

There has been an explosion in human population due to:

War, disease and famine have only been temporary reversals in the upward trend

• Birth rate • Death rate • Immigration: Individuals join a new population• Emigration: Individuals leave a population

Factors affecting Growth

Population Growth = (Births + Immigration) – (Deaths + Emigration)

Percentage Population Growth Rate: Population change during the period

Population at the start of the period X 100

• Economic conditions: Lower capita income tend to have higher birth rates

• Cultural/Religious: Some religions oppose birth control

• Social pressure: Large families can improve social standing

• Birth Control: Contraception isn't always available

• Political factors: Government influence births via education and taxation

• Age Profile: The more elderly people the higher the death rate

• Life expectancy: ECDLs have lower life expectancies

• Food supply: Need a balanced diet• Sanitation: Reduces water-borne deaths

e.g. cholera• Medical care availability• Natural disasters: Higher death rates near

droughts• War

Birth Rate FactorsBirth Rate:

number of births per year Total population in the same year X1000

Death Rate FactorsDeath Rate: number of deaths per year Total population in the same year X1000

• Well economically developed countries have a higher life expectancy, this has led to change in societies from short life expectancies to long life expectancies causing demographic transition

Population Structure

• Stable Population: Birth and death rate are balanced so no decrease or increase in population

• Increasing Population: High birth rate (shows wider base) and fewer old people (narrow apex)

• Decreasing Population: Lower birth rate (narrow base) and low mortality rate so more elderly people (wider apex)

Population pyramids can be used to plot

populations:

• Plotting as survival curve allows life expectancy to be calculatedSurvival Rates

Stable Population

Increasing Population

Decreasing Population

AQA A2 Biology Unit 4

ATP & Photosynthesis

Specification

ATP

The synthesis of ATP from

ADP and phosphate

its role as the immediate source of energy for biological processes.

Photosynthesis

The light-independent

and light-dependent

reactions in a typical C3

plant.

Light-dependent reaction

• light energy excites electrons in

chlorophyll

• energy from these excited

electrons generates ATP and

reduced NADP

• the production of ATP involves

electron transfer associated with the

electron transfer chain in chloroplast

membranes

• photolysis of water produces

protons, electrons and oxygen.

Light-independent reaction

• carbon dioxide is accepted by ribulose

bisphosphate (RuBP) to form two molecules of glycerate 3-phosphate

(GP)

• ATP and reduced NADP are required for the reduction of GP to

triose phosphate

• RuBP is regenerated in the Calvin cycle

• Triose phosphate is converted to useful organic substances.

Limiting factors

The principle of limiting factors as applied to the effects of temperature,

carbon dioxide concentration

and light intensity on the

rate of photosynthesis.

3.4.2 ATP provides the immediate source of energy for biological processes.3.4.3 In photosynthesis, energy is transferred to ATP in the light-dependent reaction and the ATP is utilised in the light-independent reaction.Candidates should be able to explain how growers apply a knowledge of limiting factors in enhancing temperature, carbon dioxide concentration and light intensity in commercial glasshouses. They should also be able to evaluate such applications using appropriate data.

Definitions• ATP: An activated nucleotide found in all living cells that acts as an energy carrier• Endothermic: Reaction that requires energy• Activation Energy: Minimum energy required to bring about a chemical reaction• Hydrolysis: The breaking of large molecules to small using water• Condensation: Chemical process where two molecules form a larger molecule• Electron carrier molecules: A chain of carrier molecules along which electrons

pass, releasing energy in the form of ATP• Thylakoids: Series of flattened membranous sacs in a chloroplast that contain

chlorophyll and the associated molecules needed for the light-dependent reaction• NADP: Molecule that carries electrons produced in the light-dependent reaction• Stomata: Pores surrounded by guard cells that allow gas diffusion• Stroma: Matrix of chloroplast where the light-independent reaction occurs

2.1 Energy and ATPAll living organisms require energy to stay alive

Plants use solar energy from the sun to combine water and CO₂ in photosynthesis

The organic molecules formed are broken down by plants and animals into ATP

• Energy can take many forms such as light and kinetic• Energy cannot be created or destroyed• It is measured in joules(J)• It can change from one form to another

Energy

• Metabolism: All reactions in the body require energy• Movement: For in and out of the body itself• Active Transport: Ions and molecules need to be transported

against the concentration gradient across plasma membranes• Repair and Division• Production of Substances: Such as enzymes and hormones• Maintenance of body temperature: Mammals and birds are

endothermic and need energy to replace that lost to the environment

Why Energy is Needed

Energy and Metabolism• 1. Light energy from the sun is converted by plants into chemical energy during photosynthesis• 2. The chemical energy from photosynthesis, organic molecules, is converted into ATP during

respiration• 3. ATP Is used by cells

Storing ATP• ATP has 3 phosphate groups which have unstable bonds thus a low activation energy so are easily

broken• Energy is released when the bonds break• The reaction uses water to is a hydrolysis reaction• ATP + H₂O → ADP + Pi (inorganic phosphate) + E (Energy)

Synthesis of ATP• Adding an inorganic phosphate to ADP can form ATP again in a condensation reaction. It occurs in 3

ways:• Photophosphorylation: In chlorophyll containing plant cells during photosynthesis• Oxidative Phosphorylation: In the mitochondria of plants and animal cells during electron transport• Substrate-level Phosphorylation: Plant and animal cells when phosphate groups are transferred

from donor molecules to ADP making ATP• In the first two ATP is synthesised using energy released during electron transfer along an electron

carrier chain

Roles of ATPATP is the immediate energy source as its energy store is not long lasting due to the instability of the

phosphate bonds

Cells don’t store large quantities of ATP however ATP is rapidly re formed from ADP and inorganic phosphate easily making it go further

ATP is better than glucose as it releases smaller more manageable quantities of energy

The hydrolysis of ATP to ADP is a single reaction releasing energy immediately whereas the process for glucose is much longer

ATP cannot be stored so is continuously made in the mitochondria, cells such as muscle fibres contain large mitochondria due to the required energy

• Metabolic Processes: Forming polysaccharides from monosaccharides, Polypeptides from amino acids and DNA/RNA from nucleotides

• Movement: Provides energy for muscle contraction allowing the muscle filaments to slide over each other

• Active Transport: ATP provides energy to change the shape of carrier proteins in plasma membranes allowing molecules to move against the concentration gradient

• Secretion: Forms lysosomes needed for secretion of cell products• Activation of molecules: When a phosphate molecule is

transferred from ATP to another it makes it more reactive lowering activation energy. This allows enzyme catalysed reactions to occur more readily

ATP as a source of energy

Absorption of Light Energy• Light energy is captured and

is transferred to chlorophyll a molecules.

• Electrons in the outer shell of the chlorophyll a molecule are excited.

• The electrons are passed through a series of carrier molecules and are used to power,– Photolysis– Reduction of NADP– Photophosphorylation

3.1 Photosynthesis• Large surface area • Leaves minimise overlapping• Thin so short diffusion path• Transparent cuticle and epidermis let light through to

photosynthetic mesophyll cells• Long narrow mesophyll cells packed with chloroplast• Large number of stomata able to open and close in light intensities• Air spaces allow diffusion of CO₂ and O₂• Xylem brings water and phloem carries away sugars

Leaf Structure

• 6CO₂ + 6H₂O → C6H12O + 6O2• 1. Capturing light energy by chloroplast pigments e.g. chlorophyll• Light-dependent Reaction: Light converted into chemical energy,

an electron flow is created and causes water to split (photolysis) into protons, electrons and oxygen. Products are reduced NADP, ATP and oxygen

• Light-independent Reaction: Protons are used to reduce carbon dioxide to produce sugars and other organic molecules

Photosynthesis Outline

• Grana formed from thylakoids house the light dependent stage. They contain chlorophyll and also attach to each other via inter-granal lamellae

• Stroma is a fluid filled matrix where the light independent reaction occurs

Structure of Chloroplast

THE LIGHT-DEPENDENT REACTION

Chlorophylla

light

e -e -

e -

e -

e -

2H2O

4H+ + e - + O2

4NADP 4NADPH

ADP + P

PHOTOLYSIS

PHOTOPHOSPHORYLATION

ATP

3.2 The Light-Dependent ReactionWhen a substance loses electrons it is oxidised

When a substance gains electrons it is reduced

• When chlorophyll absorbs light energy it causes a pair of electrons in it to become a higher energy level, they are in an excited state

• The electrons then leave the chlorophyll and are taken up by an electron carrier• The chlorophyll has become oxidised and the electron carrier reduced • Via a series of oxidation-reduction reactions the electrons pass along the electron

carriers as a transfer chain is formed in the membranes of the thylakoids• Each new carrier has a slightly lower energy level than the one before causing the

electrons to lose energy• This energy is used to combine an inorganic phosphate molecule with ADP forming

ATP

The Making of ATP

• Due to the lose of electrons the chlorophyll they must be replaced• The electrons are replaced via water molecules being split using light energy• 2H₂O → 4H+ + 4e- +O₂• The hydrogen ions are taken up by NADP causing it to be reduced• The reduced NADP and electrons from the chlorophyll enter the light independent

reaction• Reduced NADP gives the plant a source of chemical energy• The oxygen by-product from the photolysis of water is diffused or used in

respiration

Photolysis of Water

PhotolysisWater molecules are split

using energy from excited electrons in chlorophyll a molecules.

2H2O 4H+ + 4e- + O2

Oxygen is released into the atmosphere.

Hydrogen ions and electrons are now available to be used to produce a reducing agent.

Site of Light-Dependent Reaction

Origin: Thylakoids of Chloroplast

Adaptations of Chloroplast:• Thylakoid membranes provide a large surface area for

chlorophyll attachment, electron carriers and enzymes• Network of proteins in the grana hold the chlorophyll in a

precise manner for maximum absorption of light• Granal membranes have enzymes for ATP production• Contain both DNA and ribosomes so there is easy

manufacture of proteins needed

Reduction of NADP

Electrons and Hydrogen ions produced during photolysis are used to reduce NADP to Reduced NADP (NADPH).

Excited electrons and hydrogen ions are transferred to NADP.

NADP + H + + e- NADPH

NADPH can donate electrons and hydrogen ions to carbon dioxide and so is a reducing agent.

3.3 The Light-Independent ReactionIt takes place in the stroma of the chloroplasts

It doesn’t require light to occur

ATP and reduced NADP are used to reduce carbon dioxide

• Carbon dioxide from the atmosphere diffuses into the leaf through stomata and dissolves in water around the walls of the mesophyll cells. It then diffuses through the plasma membrane, cytoplasm and chloroplast membranes to the stroma

• In the stroma, CO₂ combines with ribulose bisphosphate(RuBP) using an enzyme

• Glycerate 3-phosphate (GP) is formed, 2 molecules per one combination

• ATP and reduced NADP activate the GP into triose phosphate(TP)

• The NADP is reformed and goes back to the light dependent reaction to be reduced again by accepting more hydrogen

• Some TP is converted into useful organic substances such as glucose

• Most TP is used to regenerate RuBP using ATP from the light dependent reaction

The Stages

Photophosphorylation

• Energy from the excited electrons is used to make ATP.

• A phosphate group is added to ADP.

ADP + P --energy from excited electrons ATP

Products of the Light Dependent Stage

• Photolysis– H+ ions– Electrons– Oxygen

• Photophosphorylation– ATP

Used to produce NADPH

The Calvin Cycle

Site of the Light-Independent ReactionThe chloroplast is adapted for this reaction as:

• The fluid of the stroma contains enzymes needed• The fluid surrounds the grana so the products can diffuse

quickly to it• It contains both DNA and ribosomes so can easily

manufacture proteins needed

3.4 Factors affecting Photosynthesis• A limiting factor restricts the rate at which a process can occur• It is the slowest reaction that determines the overall rate of

photosynthesis• ‘At any given moment, the rate of a physiological process is limited

by the factor that is at its least favourable value’

Limiting Factors

• When light is the limiting factor photosynthesis is directly proportional to light intensity

• As light intensity increases the volume of oxygen produced and carbon dioxide absorbed will increase till it balances the oxygen absorbed and carbon dioxide produced

• This point is the compensation point due to no net exchange of gases into or out of the plant

• When increasing light intensity has no effect on rate of photosynthesis there is another limiting factor

Light Intensity

• 0.1% CO₂ will give the optimum concentration for photosynthesis to occur

• CO₂ concentration affects enzyme activity especially the enzyme that catalyses the combination of ribulose bisphosphate and carbon dioxide in the light independent reaction

Carbon Dioxide

• From 0 to 25°C the rate of photosynthesis doubles for each 10°C • 25°C is the optimum temperature and after this the rate of

photosynthesis declines due to enzymes becoming denatured• Photosynthesis isn't purely photochemical as if it was it wouldn’t be

affected by temperature

Temperature

The Light-Independent Reaction

Does not require light energy. However, requires the products produced in the light-

dependent reaction, therefore photosynthesis cannot occur without light energy.

Takes place in the stroma.Enzyme controlled, therefore it is affected by

temperature.Uses energy from ATP, and the electrons and

hydrogen ions from NADPH to reduce CO2 to glucose.

Fixing Carbon Dioxide

• Ribulose Biphosphate (RuBP), a 5 carbon molecule, combines with carbon dioxide via the enzyme RuBISCO.

• This forms 2 molecules of glycerate-3-phosphate (GP), a 3 carbon organic acid.

Reducing glycerate-3-phosphate (GP)

NADPH and ATP from the light-dependent reaction are required for this stage.

NADPH transfers electrons and hydrogen ions to GP to form 2 molecules of Triose phosphate.

The energy for this is provided by the ATP.

The NADPH has now been oxidised back to NADP and can be reused in the light-dependent reaction.

The ATP has lost energy and so returns to ADP + P which can also be reused in the light-independent stage.

Producing Glucose and Regenerating RuBP

• For every 6 CO2 molecules entering the cycle, 12 Triose phosphates will be produced.

• 2 of these molecules will be converted into glucose.

• Of the 12 Triose phosphates that are produced, 10 will be used to regenerate RuBP.

Producing Glucose Regenerating RuBP

Law of Limiting Factors: “ The overall rate of the process will be limited by the factor which is at the least favourable value”

FACTORS AFFECTING THE RATE OF PHOTOSYNTHESIS

Light Intensity At low light intensities, the rate of

photosynthesis is directly proportional to the light intensity.

Because as more light becomes available, more chlorophyll molecules can absorb light so more electrons are excited leading to photolysis and photophosphorylation.

More ATP and NADPH are produced so the light-independent reactions can occur at a higher rate so more product is produced.

Eventually a maximum rate is reached and so increasing light intensity has no effect so the graph levels off.

This can be because all available chlorophyll molecules are absorbing light. Or some other factor is now the limiting factor.

Temperature When light is not a limiting factor (i.e. high

light intensities), increasing the temperature increases the rate of photosynthesis.

Above the optimum temperature, any further increase causes the rate to decrease rapidly.

Because the Calvin Cycle is enzyme controlled, when the temperature increases both enzymes and substrates gain kinetic energy, so more collisions occur, so more enzyme substrate complexes form, so more product forms.

When the temperature exceeds the optimum, the enzymes will denature and the specific shape of the active site will change and no longer be complementary to the substrate so fewer enzyme-substrate complexes can form.

Carbon Dioxide Concentration At low CO2 levels an increase in

concentration causes a directly proportional increase in the rate of photosynthesis.

A maximum rate is eventually reached and further increase has no effect and so the graph levels off.

This is because atmospheric CO2 levels are lower than the optimum value so when concentration is increased more CO2 is absorbed so more product is made.

Eventually, there is no more RuBP available to absorb anymore CO2 so there is no further effect.

IMPLICATIONS FOR COMMERCIAL GLASSHOUSE MANAGEMENT

What does glasshouse cultivation allow?

• Better yields can be achieved because conditions for photosynthesis can be kept at an optimum.

• Crops can be grown out of season all year providing a better economic return.

• Crops can be grown in regions where they might not grow well naturally.

Factors to be Considered For maximum yields to be achieved, limiting factors must be kept at an optimum because the

faster the plant photosynthesises the more carbohydrates it produces which means the maximum yield will be achieved in the shortest time.

Carbon dioxide levels High levels of CO 2 are the optimum however if the levels are too high over a long period of time then

the stomata will close resulting in a drop in the rate of photosynthesis. A compromise level must therefore be used.

Temperature An optimum temperature should be used to ensure that the plants photosynthesise rapidly without

any damage to cells. Water

Need to be well watered to ensure the stomata remain open to absorb CO 2. However the soil must not become waterlogged as it will reduce the uptake of mineral by active transport. The plants must not become to wet either as this will promote fungal disease to spread.

Light Artificial lighting is used when natural light intensity falls. Specific wavelengths are chosen so they are

absorbed by the plants (i.e. red and blue). Minerals

Soil must be supplemented with essential minerals. Potassium is particularly important in stomatal mechanisms and so must be kept at an optimum.

AQA A2 Biology Unit 4

Respiration

Specification

Aerobic Respiration

glycolysis takes place in the cytoplasm and involves the

oxidation of glucose to pyruvate with a net gain of

ATP and reduced NAD

pyruvate combines with coenzyme A in the link

reaction to produce acetylcoenzyme A

in a series of oxidation-reduction reactions the Krebs cycle generates

reduced coenzymes and ATP by substrate-level phosphorylation, and carbon dioxide is lost

Aerobic Respiration Conc

acetylcoenzyme A is effectively a two carbon molecule that combines

with a four carbon molecule to produce a six

carbon molecule which enters the Krebs cycle

synthesis of ATP by oxidative phosphorylation

is associated with the transfer of electrons down the electron

transport chain and passage of protons across

mitochondrial membranes.

Anaerobic respiration

Glycolysis followed by the production of ethanol or lactate

and the regeneration of NAD in anaerobic

respiration.

3.4.4 In respiration, glycolysis takes place in the cytoplasm and the remaining steps in the mitochondria. ATP synthesis is associated with the electron transfer chain in the membranes of mitochondria.

Definitions• Hydrolysis: Breaking down of large molecules into smaller ones by the addition of water• Activation Energy: Energy required to bring about a chemical reaction• Oxidation: Lose of Electrons• Glycolysis: First part of cellular respiration in which glucose is broken down anaerobically in

the cytoplasm to 2 molecules of pyruvate• Substrate-Level Phosphorylation: The formation of ATP by the direct transfer of a phosphate

group from a reactive intermediate to ADP• Aerobic: Connected with the presence of oxygen, aerobic respiration requires oxygen to

release energy from glucose and other foods• Adenosine Triphosphate: An activated nucleotide found in all living cells that acts as an

energy carrier. • Redox: Reaction in which oxidation and reduction take place• Krebs Cycle: Series of aerobic biochemical reactions in the matrix of the mitochondria of

most eukaryotic cells by which energy is obtained through the oxidation of acetylcoenzyme A produced in the breakdown of glucose

• NAD: (Nicotinamide adenine dinucleotide phosphate) Molecule that carries electrons and hydrogen ions during aerobic respiration

4.1 Respiration Overview

Glucose cannot be used directly by cells as an energy source so they use ATP

• Aerobic Respiration: requires oxygen and produces carbon dioxide, water and much ATP

• Anaerobic Respiration ((fermentation): Takes place in the absence of oxygen and produces lactate (inn animals) or ethanol and carbon dioxide in plants, very little ATP is produced

There are two different forms of respiration:

• Glycolysis: Splitting of the 6 carbon glucose molecule into 2 3-carbon pyruvate molecules

• Link Reaction: Conversion of the 3-carbon pyruvate into carbon dioxide and a 2-carbon molecule called acetylcoenzyme A

• Krebs Cycle: Introduction of acetylcoenzyme A into a cycle of oxidation-reduction reactions that yield some ATP and a large number of electrons

• Electron Transport Chain: Use of the electrons produced in the Krebs Cycle to synthesis ATP with water produced as a by-product

Aerobic Respiration steps:

GlycolysisGlycolysis is the initial stage in both aerobic and anaerobic respiration

Occurs in the cytoplasm of all living cells

A hexose sugar is split into 2 molecules of 3-carbon pyruvate

• Activation of Glucose by phosphorylation: Glucose is made more reactive by adding 2 phosphate molecules, these come from the hydrolysis of 2 ATP molecules to ADP. This provides energy to activate the glucose as the activation energy has been lowered

• Splitting of the Phosphorylated glucose: Each glucose molecule is split into 2 3-carbon molecules known as triose phosphate

• Oxidation of Triose Phosphate: Hydrogen is removed from each triose phosphate molecule and transferred to a hydrogen-carrier molecule (NAD) to form reduced NAD

• Production of ATP: Enzyme controlled reactions convert each triose phosphate into another 3-carbon molecule called pyruvate, 2 molecules of ATP are regenerated from ADP

It has four stages:

• 2 molecules of ATP• 2 molecules of reduced NAD• 2 Molecules pyruvate

Energy Yield:

As glycolysis occurs in the cytoplasm of cells it doesn’t require an organelle or membrane for it to occur

It doesn’t require oxygen and without oxygen pyruvate is converted to lactate or ethanol by anaerobic respiration

Glycolysis Glycolysis takes place in the cytoplasm

of the cell. Glucose is first phosphorylated by 2

phosphate groups from 2 molecules of ATP to produce 2 molecules of glyceraldehyde-3-phosphate (GALP).

GALP is then oxidised and dephosphorylated into pyruvate. In this process, the phosphate groups are

transferred to ADP producing 2 molecules of ATP. A hydrogen is transferred to a molecule of NAD producing NADH.

The net yield of glycolysis per glucose is 2ATP 2NADH 2 pyruvate

The pyruvate produced then diffuses into the mitochondria.

1 x Glucose

2 x Glyceraldehyde3-phosphate

2 x Pyruvate

2ATP

2ADP + 2P

4ATP

4ADP + 4P

2NAD

2NADH

4.2 The Link ReactionFor pyruvate molecules to enter the Krebs cycle they need to by oxidised

Occurs in the mitochondria

Pyruvate produced in the cytoplasm is actively transported into the matrix of mitochondria

• Hydrogen is removed from the pyruvate, the hydrogen is accepted by NAD to form reduced NAD

• 2-carbon molecule, acetyl group, is formed and then combines with coenzyme A ((CoA) to produce acetylcoenzyme A

• A carbon dioxide molecule is formed from each pyruvate

Pyruvate undergoes a series of reactions:

Pyruvate + NAD + CoA → acetyl CoA + reduced NAD + CO₂

The Link Reaction Takes place in the matrix. Pyruvate undergoes oxidative

decarboxylation. Oxidation

Electrons and hydrogen from the pyruvate are transferred to NAD producing NADH.

Decarboxylation Carbon dioxide is removed which converts the

pyruvate into acetate. The acetate then combines with

CoenzymeA to produce Acetyl CoenzymeA. Since 2 molecules of pyruvate were

produced in glycolysis, the net yield of the link reaction per glucose is 2 Acetyl CoenzymeA 2NADH 2 Carbon dioxide

2 x Pyruvate

Acetyl CoenzymeA

NAD

NADH

Carbon dioxide

CoenzymeA

The Krebs CycleSeries of oxidation-reduction reactions in the matrix of mitochondria

• 2-carbon acetylcoenzyme A from the link reaction combines with 4-carbon molecule to produce a 6-carbon molecule

• The 6-carbon molecule loses carbon dioxide and hydrogen to give a 4-carbon molecule and a single ATP molecule produced as a result of substrate-level phosphorylation

• The 4-carbon molecule can now be combined with another acetylcoenzyme A to repeat the cycle

Process:

• Reduced coenzymes e.g. NAD/FAD have the potential to produce ATP molecules• 1 molecule of ATP• 3 molecules of carbon dioxide

Products:

Due to 2 pyruvate molecules being produced from each original glucose the yield of a single glucose molecule is double the quantities above

• Major role in photosynthesis and respiration as carry hydrogen atoms from one molecule to another e.g.

• NAD, important throughout respiration• FAD, important in the Krebs cycle• NADP, important in photosynthesis• NAD is the most important carrier, it works with dehydrogenase enzymes that

catalyse the removal of hydrogen ions from substrates and transfers them to other molecules such as hydrogen carriers involved in oxidative phosphorylation

Coenzymes: some enzymes require to function

• It breaks down macromolecules into smaller ones e.g. pyruvate into carbon dioxide• It produces hydrogen atoms carried by NAD to the electron transport chain for

oxidative phosphorylation . This leads to the production of ATP for metabolic energy in the cell

• It regenerates 4-carbon molecule that combines with acetylcoenzyme A • It is a source of intermediate compounds used by cells to manufacture substances

such as fatty acids and chlorophyll

Significance of the Krebs Cycle

The Krebs Cycle• Takes place in the matrix.• Closed cycle of enzyme controlled reactions.• Provides a continuous supply of reduced electron

carriers for the electron transport chain.• AcetylCoA combines with a 4-C compound to produce

citric acid, a 6-C compound.• The citric acid then undergoes

– A decarboxylation reaction which removes carbon dioxide.– A series of oxidation reactions which remove hydrogen ions

and electrons. H + ions and e – are picked up by NAD and FAD and they become NADH and FADH.

• At the end of the cycle the 4-C compound is recycled so the cycle can continue.

• Since each glucose molecule produced 2 molecules of pyruvate and so 2 molecules of AcetylCoA, the yield per glucose for the Krebs cycle is– 4 carbon dioxide– 2FADH– 6NADH– 2ATP

ADP

ATP

NADH

NADH

NADH

FADH

4.3 Electron Transport ChainOccurs in the mitochondria

Enzymes are attached to the cristae that are involved in the electron transport chain

• Hydrogen atoms produced in glycolysis and the Krebs cycle combine with coenzyme NAD and FAD that are attached to the cristae

• Reduced NAD and FAD donate the electrons of the hydrogen atom to the first molecule in the electron transport chain

• This releases the protons from the hydrogen atoms and these are actively transported across the inner mitochondrial membrane

• The electrons pass along the chain via oxidation-reduction reactions in which they lose energy that combines ADP and an inorganic phosphate to make ATYP, remaining energy is given off as heat

• The protons accumulate in the space between the mitochondrial membranes before they diffuse back into the matrix through special protein channels

• At the end electrons combine with the protons and oxygen to form water

Synthesis of ATP

• It is the final acceptor of hydrogen atoms • Without it the hydrogen ions and electrons would ‘back up’ along the chain and

respiration would cease• Cyanide is a non-competitive inhibitor of the final enzyme in the electron transport

chain • It catalyses the addition of the hydrogen ions and electrons to oxygen to form water• Its inhibition causes hydrogen ions and electrons to accumulate on the carriers

stopping cellular respiration

Importance of Oxygen

Electron Transport Chain Found on the cristae of the mitochondria

which provide a large surface area for this to take place.

The electron carriers are arranged in descending energy levels.

When electrons pass through the carriers, the energy released is used to move hydrogen ions from the matrix into the intermembrane space.

This creates a large concentration gradient of H+ ions and so they diffuse back into the mitochondrial membrane by diffusion via ATP synthase.

As the H+ ions diffuse through the enzyme, they attach P groups to ADP to produce ATP.

At the end of the chain, the electrons are picked up by the terminal electron acceptor, which is oxygen, to produce water.

2e - + 2H + + ½O2 H2O This process is called oxidative

phosphorylation.

4.4 Anaerobic Respiration

Without oxygen the Krebs Cycle and the Electron Transport Chain cannot occur

Only glycolysis is a source of ATP, for it to continue its products of pyruvate and hydrogen must be constantly removed

The hydrogen must be released from the reduced NAD in order to regenerate NAD as if it wasn’t converted no NAD could take up the newly produced hydrogen from glycolysis and it would stop

The replenishment of NAD is achieved by pyruvate accepting hydrogen from the reduced NAD

• Bacteria, fungi and plants can produce ethanol• The pyruvate molecule formed in glycolysis loses a molecule of carbon

dioxide and accepts hydrogen from reduced NAD to produce ethanol• Yeast is grown in anaerobic conditions to produce ethanol for brewing

• Pyruvate + reduced NAD → Ethanol + Carbon dioxide + NAD

Production of Ethanol

• Anaerobic respiration I animals leads to lactate production in order to overcome temporary shortage of oxygen

• Lactate production occurs most commonly in muscles as a result of strenuous exercise as there is not enough oxygen being supplied causing an oxygen debt

• Reduced NAD must be removed in order for energy to be released • This is achieved as each pyruvate molecule produced takes up 2 hydrogen

atoms from the reduced NAD produced in glycolysis to form lactate• Lactate needs to be oxidised back to pyruvate • It can either further to release energy or converted into glycogen • Lactate build up can cause cramp and muscle fatigue. Muscles do have a

certain tolerance however it has to be removed by the blood and taken to the liver to be converted to glycogen

• Pyruvate + reduced NAD → lactate + NAD

Production of Lactate

• In anaerobic respiration, pyruvate is converted to either ethanol or lactate.• Therefore in anaerobic respiration neither the Krebs cycle nor the electron

transport chain can take place• The only ATP that can be produced anaerobic respiration is formed by

glycolysis which is a very small amount compared to aerobic respiration

Energy Yields

ANAEROBIC RESPIRATION

1 x Glucose

2 x Pyruvate

2NAD

2NADH

2NADH

2NAD

2 x Lactic Acid

2ATP

2ADP + 2P

Anaerobic Respiration

When oxygen isn’t available, the electron transport chain cannot operate so the initial supply of NAD run out.

To regenerate this, pyruvate produced during glycolysis must be reduced.

Pyruvate is converted into lactic acid in animal cells.Pyruvate + NADH Lactic AcidThe net yield from anaerobic respiration is simply the

2ATP produced in glycolysis and is therefore much less energy efficient.

In some plants and microbes, pyruvate is converted into ethanol.

Pyruvate + NADH Ethanol + Carbon Dioxide + NAD

AQA A2 Biology Unit 4

Nutrient Cycles

Specification

Nutrient cycles

The role of microorganisms in the carbon and nitrogen

cycles in sufficient detail to illustrate the

processes of saprobiotic nutrition,

ammonification, nitrification, nitrogen

fixation and denitrification.

Carbon

The importance of respiration,

photosynthesis and human activity in giving

rise to short-term fluctuation and long-term change in global

carbon dioxide concentration.

The roles of carbon dioxide and methane in

enhancing the greenhouse effect and bringing about global

warming.

Nitrogen

The environmental issues arising from the use of

fertilisers.

Leaching and eutrophication.

3.4.6 Chemical elements are recycled in ecosystems. Microorganisms play a key role in recycling these elements.Candidates should be able to analyse, interpret and evaluate data relating to evidence of global warming and its effects on the yield of crop plants, the life-cycles and numbers of insect pests, the distribution and numbers of wild animals and plants.Candidates should be able to analyse, interpret and evaluate data relating to eutrophication.

Definitions• Active Transport: Movement of a substance across a membrane from a region of

low concentration to high concentration using ATP

• Aerobic: In the presence of oxygen

• Anaerobic: Without oxygen

• Biomass: Total mass of living material in a specific area at a given time, usually measured as dry mass since water value is variable

• Consumers: Organism that obtains energy by eating another

• Decomposer: An organism, e.g. fungus that breaks down organic material.

• Ecosystem: Unit in ecology made up of all interacting biotic and abiotic factors in a specific area

• Greenhouse Gas: Such as methane and carbon dioxide, they cause heat to be trapped in the atmosphere raising the Earth’s temperature

• Niches: All conditions and resources required for an organism to survive, reproduce and maintain population

• Oxidation: Chemical reaction causing the loss of electrons

• Producers: Organism that synthesises organic molecules from simple inorganic ones

• Saprobiotic Microorganisms (Saprophyte): Organism that obtains food from dead or decaying remains of other organisms

Basic Nutrients Cycle• The flow of nutrients such as carbon and nitrogen is cyclic

Nutrients taken up by producers

(plants) as simple inorganic molecules

Producers incorporates the

nutrient into complex organic

molecules

The producer is eaten and

nutrients pass to the consumers

The nutrients are then passed along

a food chain

When both the producer and consumer die

saprobiotic microorganisms break down the

molecules releasing the nutrients

6.1 The Carbon Cycle

The main source of carbon for terrestrial organisms is carbon dioxide in the atmosphere

Photosynthetic organisms remove it from the air to form macromolecules e.g. carbohydrates, fats and proteins

Respiration returns carbon dioxide back to the air

The concentration of CO₂ is higher at night than day due to no photosynthesis occurring while respiration still occurs

The Increase in Carbon Dioxide• Combustion of Fossil Fuels: Coal, oil and peat

releases CO₂ previously trapped• Deforestation: Removes photosynthesising biomass

so less CO₂ is removed

Main Reasons due to human activities:

CO₂ is a greenhouse gas and contributes to global warming

The ocean is a CO₂ sink so keeps it constant

• The decomposers then absorb the molecules via diffusion

When organisms die Saprophytes break them down into small soluble molecules using enzymes

The carbon is then released as CO₂ during respiration of the decomposer

When decay is prevented fossils are formed

The Carbon Cycle Diagram

6.2 The Greenhouse Effect and Global Warming• Natural process that occurs all the time• Due to solar radiation from the sun reaching the

earth • Greenhouse gases trap the heat in the Earth’s

atmosphere causing it to heat up

The Greenhouse Effect

• The major greenhouse gas is CO₂ which is increasing due to human activities

• Methane is also produced when microorganisms break down organic molecules , it occurs in two situations:• Decomposers break down dead remains of

organisms• Microorganisms in intestines of primary

consumers e.g. cattle digest food

Greenhouse Gases

• Due to the layer of greenhouse gases building up it traps the heat from the sun causing the Earth to heat up

Global Warming

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Consequences of Global WarmingChanges in temperature and precipitation, the timing of seasons and frequency of

extreme events e.g. storms

Climate change will effect niches available due to organisms being adapted to particular niches

Animals could migrate to new areas causing competition and loss of native species

Melting ice gap could cause extinction of wild plants and animals e.g. polar bears and sea levels will rise

Low land would be flooded and sea water would extend further up rivers making cultivation difficult

Droughts could occur due to higher temperatures meaning xerophytes could only survive

Greater rainfall would occur in some areas

Insect lifecycles will be altered and due to them carrying human and crop pathogens tropical diseases could spread toward poles

Benefit could be more rainfall filling reservoirs, higher temperatures causing higher rate of photosynthesis so more productivity and a larger harvest

6.3 The Nitrogen Cycle

All living organisms require a source of nitrogen to form nucleic acids and proteins

Plants take most of their nitrogen up via nitrate ions (NO₃-) from the soil

The ions are absorbed by active transport from the root hairs

Animals obtain their nitrogen compounds by eating the plants

Nitrate ions are soluble

When plants and animals die decomposition occurs and the nitrates are restored to the soil

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The Stages of the Nitrogen CycleAmmonification

• The production of ammonia from organic ammonium compounds e.g. urea, proteins and nucleic acids• Saprobiotic microorganisms e.g. fungi feed on these materials releasing ammonia which forms ammonium ions in

the soil • This is where nitrogen returns to non living components of the ecosystem

Nitrification• Ammonium ions to nitrate ions is an oxidation reaction so releases energy • It is carried out by nitrifying bacteria in two stages:• 1. Oxidation of ammonium ions to nitrite ions (NO₂¯) • 2. Oxidation of nitrite ions to nitrate ions (NO₃¯)• Nitrifying bacteria require oxygen to carry out the conversions so the soil needs to have air spaces • Farmers keep soil light and aerated by ploughing and having good drainage

Nitrogen Fixation• Nitrogen gas is converted to nitrogen containing compounds • 1. Free living nitrogen fixing bacteria reduce gaseous nitrogen to ammonia to manufacture amino acids, when the

bacteria dies and decay they release the nitrogen compounds• 2. Mutualistic nitrogen fixing bacteria live in nodules on roots of plants and they obtain carbohydrates from the

plant while in return the plant acquires amino acids from the bacteria

Denitrification• When soil is waterlogged there is a shortage of oxygen and the type of microorganism present changes• Fewer aerobic nitrifying and nitrogen fixing bacteria are found meaning more anaerobic denitrifying bacteria are

present• This bacteria converts soil nitrates into gaseous nitrogen reducing availability of nitrogen containing compounds for

plants • To prevent the build up of denitrifying bacteria the soil has to be well aerated

6.4 Use of Natural and Artificial Fertilisers

Intensive food production makes large demands on the soil

Due to this the minerals are removed from the soil, in agriculture the remains of the consumer are rarely returned to the same area so mineral ions fall

• Natural (organic): consist of dead/decaying remains as well as animal waste

• Artificial (inorganic): Mined from rocks and deposits then converted into different forms to give the appropriate balance of minerals , compounds contain nitrogen, phosphorus and potassium

The mineral ions need to be replenished so

fertilisers are added

Fertilisers Increasing Productivity

Plants require minerals for growth, nitrogen is needed for proteins and DNA

With nitrogen plants grow taller and have a greater leaf area

This increases the rate of photosynthesis and improves crop productivity

6.5 Environmental Consequences of using Nitrogen Fertilisers

Effects of Nitrogen Fertilisers• Nitrogen is essential for proteins and growth and causes the

increase in leaf area• This increases the rate of photosynthesis and improves crop

productivity

The nitrogen containing fertilisers have bad effects to: • Reduced species diversity as nitrogen rich soils favour growth

of grasses so they out compete other species that then die• Leaching leads to pollution of watercourses• Eutrophication caused by leaching of fertiliser into

watercourses

Leaching and Eutrophication• The process by which nutrients are removed from the soil • Rain water will dissolve soluble nutrients e.g. nitrates and carry them into the soil

beyond plant roots• The leached nitrates reach the watercourses e.g. rivers that drain into freshwater

lakes • They can harm drinking water, prevent efficient oxygen transport in babies and

cause stomach cancer • The leached nitrates are harmful to environment as they cause eutrophication

Leaching

• The process by which nutrients build up in bodies of water • Most rivers contain low nitrate levels so it is a limiting factor for plant/algae

growth• Nitrate concentration increases due to leaching so the plants grow exponentially• Algae grow at the surface so the upper layers of water become densely

populated with algae, ‘algae bloom’• The layer absorbs light and prevents it from reaching the lower depths• Light becomes the limiting factor for growth so plants at deeper depths die• The lack off dead plants and algae is no longer limiting for the growth of

saprobiotic algae so they grow exponentially • Saprobiotic bacteria require oxygen for respiration creating a demand for oxygen• The concentration of oxygen in the water is reduced and nitrates are reduced

from decaying organisms• Oxygen then becomes the limiting factor for aerobic organisms e.g. fish so they

die• Without aerobic organisms there is less competition for anaerobic organisms • These organisms further decompose dead material realising more nitrates and

toxic waste like hydrogen sulphide• Animal slurry, human sewage, ploughing and artificial fertilisers cause leaching

Eutrophication

AQA A2 Biology Unit 4

Ecological Succession

Specification

Succession

Succession from pioneer species to climax

community.

At each stage in succession, certain species may be

recognised which change the environment so that it becomes more suitable for

other species.

The changes in the abiotic environment result in a less

hostile environment and changing diversity.

Conservation of habitats frequently involves

management of succession.

Candidates should be able to

• use their knowledge and understanding to

present scientific arguments and ideas

relating to the conservation of species

and habitats

• evaluate evidence and data concerning issues

relating to the conservation of species

and habitats and consider conflicting

evidence

• explain how conservation relies on

science to inform decision-making.

3.4.7 Ecosystems are dynamic systems usually moving from colonisation to climax communities in the process of succession.

Definitions• Ecosystem: More or less a self-contained functional unit in ecology made up of all

the biotic and abiotic factors of a specific area

• Abiotic: An ecological factor that makes up part of the non-biological environment of an organism e.g. temperature

• Biotic: An ecological factor that makes up the living environment e.g. food

• Communities: The organisms of all species that live in the same area

• Deciduous: Plants that shed their leaves in one season

• Habitats: The place where an organism lives, characterised by physical conditions and the species of other organisms present

• Climax Community: The organisms that make up the final stage of ecological succession

• Biodiversity: The range and variety of living organisms within a particular area

• Biomass: The total mass of a living material in a specific area at a given time, usually measured as dry mass as amount of water is variable

• Conservation: The management of the Earth’s natural resources

7.1 SuccessionEcosystems constantly change, this is known as succession

The first stage of succession is the colonisation of an inhospitable environment by the pioneer species

• Product vast quantities of wind dispersed seeds/spores• Rapid germination of seeds on arrival• Ability to photosynthesise • Ability to fix nitrogen from the atmosphere • Tolerant of extreme conditions

Pioneer Species Adaptations:

• Over these stages the environment becomes more hospitable and new species begin to grow which can outcompete other species

• The pioneer species e.g. lichen, grow in inhospitable environments and as time progresses the lichen die and decompose producing nutrients to support the community

• Lichens have changed the abiotic environment by creating soil and nutrients• Mosses are the next followed by ferns causing an increase in organic matter, due to

the dying plants the soil becomes thicker• The hospitability is increased till the ultimate community is formed (climax

community) • Due to the variation of plants a variation of animals is also increased

Succession Stages

• Non-living environment becomes less hostile due to nutrients being increased• Greater number and variety of habitats• Increased biodiversity • More complex food webs• Increased biomass

Succession Features:

Climax Communities

• Have a stable equilibrium with the climate• Abiotic factors determine the dominate species in the community

Secondary Succession

• If land has been cleared for agriculture or a forest fire the process of succession still occurs

• It is a faster process as spores and seeds remain alive in the soil and there is an influx of animals and plants via migration

• There is no need for a pioneer species

7.2 Conservation of Habitats

Conservation involves active intervention from humans to maintain biodiversity

• Ethical: Species should be allowed to coexist with humans• Economic: Living organisms have a large pool of genes that

could be valuable. Long term productivity is greater if ecosystems are maintained

• Cultural and Aesthetic: Habitats and their organisms enrich our lives

Reasons for conservation:

• Many of the organisms present in the series of succession are no longer present at the climax community

• Due to being outcompeted or their habitat being no more the species often migrate

• In order to combat this problem succession is stopped e.g. the land my be burnt or grazed on by sheep stopping tree saplings from growing

• If the factor preventing further succession is removed then the climax community will grow in secondary succession

Managing Succession