Topic 5 Notes

2 Describe the structure of chloroplasts in relation to their role in

photosynthesis.
Double membrane called the chloroplast envelope
Thylakoid - Interconnected membrane bound sacs. Membrane is the site of
the Light Dependent reactions.
Photosystems - Within membrane of thylakoid, used to capture light energy
Stroma - Matrix like fluid of the chloroplast. Enzymes, sugars, organic acids
and oil droplets within. Site of Light Independent Reactions
Grana - Stacks of thylakoids, forming penny like towers.
Chlorophyll - Pigment within chloroplast, attached to photosystems, used
for the Light Dependent reactions (provides electrons used for ETC)
3 Describe the overall reaction of photosynthesis as requiring energy from
light to split apart the strong bonds in water molecules, storing the hydrogen in
a fuel (glucose) by combining it with carbon dioxide and releasing oxygen into
the atmosphere.
Requires energy in the form of ATP (active process)
Light energy used to break hydrogen bonds in water molecules
This releases oxygen
Energy is stored in glucose until plants release it by respiration
6CO2 + 6H2O (+ energy) -> C6H12O6 + 6O2
4 Describe the light-dependent reactions of photosynthesis including how light
energy is trapped by exciting electrons in chlorophyll and the role of these
electrons in generating ATP, and reducing NADP in photophosphorylation and
producing oxygen through photolysis of water.
Light energy excites 2 e in the chlorophyll molecules of PSII to a higher
energy level
When the 2 es reach their ground state, they are passed along the ETC via
a series of redox reactions
The energy released from the 2es movement from one electron carrier to
the next results, in protons being pumped across the membrane via chemiosmosis
This sets up a concentration gradient of H+ ions across the membrane
(more H+ in intermembrane space)
The flow of H+ into ATP synthase molecule phosphorylates ATP from ADP
and Pi
2 es reach PSI and are used to reduce NADP to NADPH2
Water molecule is split by light energy (photolysis) to form 2 es, to replace
the ones lost via the ETC, to 2 H+ to reduce another NADP to NADPH2
O2 is also released into the atmosphere to form O2.

 Cyclic phosphorylation More NADPH produced, as electrons from

PSI is passed to electron carriers to be used in PSII. ATP is formed, and
electrons return to PSI
Non-cyclic phosphorylation - Electrons from PSI, pass on to an electron
carrier to reduce NADP to NADPH

5 Describe how phosphorylation of ADP requires energy and how hydrolysis

of ATP provides an immediate supply of energy for biological processes.
Phosphorylation - Adding a phosphate to a molecule
Hydrolysis - Adding water to split up another molecule (removing a
phosphate)
ADP and Pi and energy (via ATP synthase) gives ATP
This is phosphorylation
ATP is an energy storage molecule it can be rapidly hydrolysed (via ATPase)
The breaking of the P-P bond releases energy
This energy generates ADP and Pi
Energy from hydrolysis of ATP used for metabolic processes
Used for muscle contraction, active transport, respiration, photosynthesis
6 Describe the light-independent reactions as reduction of carbon dioxide using
the products of the light-de
pendent reactions (carbon fixation in the Calvin cycle, the role of GP, GALP, RuBP
and RUBISCO) and describe the products as simple sugars that are used by
plants, animals and other organisms in respiration and the synthesis of new
biological molecules (including polysaccharides, amino acids, lipids and nucleic
acids).
Products of Light Dependent are 4ATP, 2NADPH
CO2 (1C) joins to RuBP (5C) with the co enzyme RUBSICO
[This forms a 6C unstable intermediate]
Breaks down to form two molecules of GP (each 3C)
These are reduced by NADPH2 (which is oxidised to NADP)
This is also phosphorylated (by the hydrolysis of ATP)
This forms 2 molecules of GALP (3C)
2 molecules of GALP (6C in total) can be used to generate one molecule of
glucose
Cycle can be repeated to generate more molecules of GALP
These can be used to generate polysaccharides, amino acids, lipids and
nucleic acids
RuBP is regenerated after the synthesis of GALP
Five out of six molecules of GALP are used for the regeneration of RuBP
ATP is hydrolysed to form RuBP
This can recombine with CO2 to start the cycle again
7 Carry out calculations of net primary productivity and explain the relationship
between gross primary productivity, net primary productivity and plant
respiration.
Gross Primary Productivity - The rate at which energy is incorporated into
producers

 Net Primary productivity - The rate at which energy taken in by producers

is incorporated into new plant biomass and is available for the next trophic level
Plant Respiration - The energy taken in by producers which is released
through metabolic processes (heat given off)
GPP= NPP + R
NPP=GPP-R
R= GPP-NPP
Units is kJ m-2 year-1
GPP could be high because
High temperatures
High rate of photosynthesis
High CO2 levels
High light intensity
8

Calculate the efficiency of energy transfers between trophic levels.

Energy enters the ecosystem through photosynthesis
Some of this Energy is incorporated into producers (plants)
A food chain develops as each trophic level of consumers eat other
consumers
Food chains and food webs show how energy can be transferred through an
ecosystem
Food chains shows lines of transfer whereas food webs show how many
food chains can overlap
Organic matter that cannot be eaten that contains energy (e.g faeces and
bone) are taken up by decomposers
Decomposers will break down this material in detritus and release CO2 into
the atmosphere
Not all energy is transferred to the next energy level
Sun (all available energy) Producer
Sunlight may carry the wrong wavelength
Sunlight may be reflected off the leaf
Sunlight hits parts of the plant which do not photosynthesise
Some light passes straight through the leaves
Producer Consumer
Parts of food e.g bones and roots are not eaten
Some parts of food are indigestible and are excreted as
waste

9
Discuss how understanding the carbon cycle can lead to methods to
reduce atmospheric levels of carbon dioxide (including the use of biofuels
and reforestation).
In Carbon cycle, CO2 from the atmosphere is taken up by plants for
photosynthesis
This is converted into organic Carbon molecules, which is eaten by
animals and passed along food chains
Animals excret inorganic Carbon

 When animals and plants die, they decay and decompose via
decomposers which eat detritus and respire CO2 into the atmosphere
Carbon escapes into the soil via fossilisation
Carbon in ocean can be incorporated into shells of organisms
Some CO2 from the atmosphere dissolves in oceans through diffusion
Fossil fuels are burnt for anthropogenic activity via combustion
releasing CO2
Carbon sinks are reservoirs of Carbon that have been stored for an
indefinite period of time
These can be found in oceans and land
These were once separate from the carbon cycle and are now
exploited by humans (e.g. Fossil fuel usage)
Biofuels can be used to reduce atmospheric levels of CO2
These are fuels made from plant based sources.
The production and burning of these fuels are carbon neutral
Carbon neutral means that there is no or little significance difference
between the level of carbon emitted into the atmosphere and the level of
carbon taken up by plants
Reforestation is the planting of new trees to replace the ones lost
This restores the carbon neutrality and carbon offsetting
Plants take up CO2 for photosynthesis
Non edible sources are favoured because they do not affect food
supply
Biofuels are also cheaper
10 Explain that the numbers and distribution of organisms in a habitat are
controlled by biotic and abiotic factors.
Biotic factors - Living features of an ecosystem
Abiotic factors - Nonliving features of an ecosystem

Biotic

Abiotic

Predation

Light

Competition

Oxygen availability

Disease

Temperature

Territory

Soil: moisture content and pH

Biotic factors
1. Predation - Populations of predators are directly linked to the populations
of prey. (positively correlated)
2. Interspecific competition - Different species compete to occupy one
particular niche in a habitat. This means resources for both populations are
reduced, so less energy will be available for growth and reproduction, decreasing
the populations of both species.
3. Intraspecific competition - Individuals of the same species compete for
resources. Both populations compete for the same resources, which then becomes
limited, so as a result the population begins to decline. As the population gets
smaller, there is less competition for resources as the population get smaller,
population grows again.
4. Territory - Area defended by a particular population of organisms to make
sure breeding pair has sufficient resources to raise their young.
5. Parasitism and disease - Diseased animals are weakened and may not
reproduce successfully. Sick predators may not be able to hunt well. Diseased prey
animals are more likely to be caught. Parasites and disease will spread more
quickly when there is a high population density. Higher biodiversity means disease
will have less effect on the community as a whole.
Abiotic factors
1. Light Intensity - Affects rate of photosynthesis in plants. This can affect
their growth and hence, the population available for animals to eat.
2. Temperature - Affects the rate of reaction with enzyme controlled
reactions (such as hatching of eggs) If optimum temp, less energy is used up to
maintain their core body temp. More energy for growth and reproduction.
Population will increase

3. Water availability - Affected by the amount of precipitation, rate of

evaporation and edaphic factors. Unless organisms have adaptation for water
supply, organisms can die without water supply.
4. Edaphic factors - Structure of soil affect plant populations ( Sand is loose,
less prone to waterlogging and light, loam is ideal and heavier, less prone to
leaching) Leaching is when water passes through quickly draining soil of
minerals needed by plants.

11 Describe how to carry out a study on the ecology of a habitat to

produce valid and reliable data (including the use of quadrats and

transects to assess abundance and distribution of organisms and the

measurement of abiotic factors, eg solar energy input, climate,
topography, oxygen availability and edaphic factors).
Measuring abundance of organisms in a habitat:
Choose a small area within a particular area to investigate
Samples picked by random (avoids bias) Use random number generator for
coordinates.
Place a quadrat (frame or point) at the random coordinates
Number of individuals in a species is counted in each quadrat
Repeat process to take many samples (to make more reliable data for a
valid conclusion)
Obtain average from data to work out individuals for the whole area.
Multiply by the size of the whole area . Percentage cover can be estimated by
taking the average of all samples.
Measuring distribution of organisms in a habitat
Select a small area within a particular area to investigate
Set up a transect
a. Line Tape measure placed along transect and
species touching transect are recorded
b. Belt Data collected using frame quadrats net to
each other along a transect
c. Interrupted Tale measurements from quadrat at
separate intervals along transect (every other 2m)
Number of individuals are counted in each quadrat
Repeat process to take many samples (to make more reliable data for a
valid conclusion)
Obtain average from data to work out individuals for the whole area.
Multiply by the size of the whole area . Percentage cover can be estimated by
taking the average of all samples.
Types of sampling
Systematic --> taken at fixed intervals. Used for observing change of conditions in habitat
Random --> every possible sample has an equal chance of selection
Measurement of Abiotic factors
1. Climate Temp is measured with a thermometer. Rainfall is measured
with a rain gauge. Vol. of water collected is measured. Humidity measured with
an electronic hygrometer.
2. Oxygen availability - Measure in aquatic habitats. Oxygen sensor for vol of
O2 dissolved in water
3. Solar input - Light sensor

4. Edaphic factors - pH measured with indicator fluid. Change in colour

compared with pH chart. Moisture content measured using difference in mass
before and after drying out a sample in oven
5. Topography - Relief - taking height readings using GPS at different points.
Slope angle - Clinometer. Aspect - using compass.
12 Explain how the concept of niche accounts for distribution and abundance of
organisms in a habitat.

Organisms exist in a habitat where the conditions are suitable for their
role in a habitat (including its abiotic and biotic interactions)
Each species has an unique niche to occupy (e.g. hunting at night in trees,
dormant at night)
When populations of 2 different species occupy the same niche, this leads
to interspecific competition
This is because both species are using up the same resources (food and
space), so there will not be enough for both species
This means that eventually the population of both will decrease due to lack
of food resources, so less energy available for reproduction and growth
Eventually one species will outcompete and the other species will decrease
When two populations of the same species occupy the same niche, this is
called intraspecific competition.
At first there is a decrease as the resources are being used up by both
populations so it becomes limiting

Eventually the population begins to grow again, as there is a smaller

population so there is less competition for space and food. This means there is
more energy for growth and reproduction.
13 Describe

time.

the concept of succession to a climax community.

Ecological succession is the process by which an ecosystem changes over
Biotic conditions change as the abiotic conditions change.
Succession occurs in seral stages

PRIMARY
1. Pioneer species (e.g Lichens) colonise on land surface. Abiotic conditions
are harsh and the pioneer species changes them. When they die and decompose
they form the first layer of soil.
2. Less hostile conditions (soil more likely to retain water) lead to mosses
forming on top of the first layer of soil and changing the abiotic conditions again,
making them less hostile.
3. Over time, more layers of soil are formed from the decay of species
forming more layers of soil, becoming more saturated with nutrients and water
(less hostile)
4. Larger plants and shrubs begin to grow, increasing biodiversity.
5. Trees grow and eventually outcompete smaller plants
6. Forms a stable climax community.

Climax Community - Most advanced community that an ecosystem can support.

Primary Succession No previous community in area before, only newly formed
or exposed.
Secondary Succession Previous community occupied before but cleared of
plants, nutrient rich soil already formed.
Different communities have different climax communities due to
differences in climate
Succession can prevented by human activity, therefore affecting the
outcome of the climax community.
This is called a plagioclimax.

14 Outline the causes of global warming including the role of greenhouse

gases (carbon dioxide and methane, CH4 ) in the greenhouse effect.
Greenhouse effect is not caused by Global warming
In the greenhouse effect, light energy from the Sun hits the surface of the
Earth
Some of the energy is absorbed by the Earth
Some of the energy escapes into Space as infrared radiation
A small amount of infrared radiation is trapped and reflected from the Earths
surface
This causes the Earths global temperature to rise
An the
increase
in global
the concentration
increases
Earths
temperatureof greenhouse gases in the atmosphere
Less Carbon Dioxide is used by photosynthesis
This is Global Warming
Greenhouse gases include, Methane, CO2, water vapour, O3 and Nitrous Oxides
Anthropogenic
activity
(human activity) increases the concentration of
Greenhouse
gases in the
atmosphere
This increases the effects of Global warming
15 Describe the effects of global warming (rising temperature, changing rainfall
patterns and seasonal cycles) on plants and animals (distribution of species,
development and life cycles).
1. Rising Temperature
Increase in enzyme activity to optimum temp (until optimum
where it decreases)
Distribution of species - Will change environmental conditions for
some species forcing them to move habitat

 Development & Life Cycles - Metabolic rate will increase, so life

cycle will be quicker. If conditions are too high, metabolic rate will decrease,
causing the life cycle to be shorter
2. Changing rainfall patterns
Distribution of species - If less rainfall is present, can lead to
species that are not adapted to living in that environment to move or die out.
Development & Life Cycles - Will affect length of dormancy of
animals. Will affect length of seasons (drier summers)

3. Seasonal Cycles
Distribution of species - Can affect the migration of animals and
production of insects and flowering
Development & Life Cycles - Will affect hatching rate
16 Explain the effect of increasing temperature on the rate of enzyme activity in
plants, animals and micro-organisms.
Enzymes Biological catalysts which increase the rate of reaction by
lowering the activation energy
Increase in temperature (optimum) Increases the amount of kinetic
energy in enzyme and substrate
More successful collisions, therefore more enzyme-substrate complexes formed

In plants animals and microorganisms

Life cycles Increase in temp, increases rate of reaction
quicker metabolic rates
quicker life cycles
quicker hatching rates
Temperature above (optimum)
Denatures enzymes
Some animals cannot hatch
Quick life cycles

17 Describe how to investigate the effects of temperature on the

development of organisms (eg seedling growth rate, brine shrimp hatch
rates).
Brine Shrimp

hatch rates
Set up water baths at a range of temperatures (0, 10, 20, 30 ,40, 50)
Control the number of eggs in each beaker - 10
Place 10 each in beakers at temperatures for 2 days
Record the number hatched every 5 hours
Control the vol of water in each beaker/salinity/oxygen
Number of hatches/ hours = rate

Seedling growth rate

Measure the height of seedlings in soil tray
Incubate seeds at different temperatures
Control water content, light intensity, CO2 concentration, incubation period
Measure change in heights
Change in height/incubation period = rate

18 Analyse and interpret different types of evidence for global warming and its
causes (including records of carbon dioxide levels, temperature records, pollen in
peat bogs and dendrochronology) recognising correlations and causal relationships.

Evidence for Global warming include Ice cores, Temperature records, Pollen in

peat bogs and dendrochronology

Ice cores contain layers of compressed snow and air bubbles of CO2. This can
be used to measure CO2 concentration over long periods of time
Temperature records can be recorded from using a thermometer in different
geographical regions. Often shows fluctuations but shows the change in temp over
time
Early records are not reliable
Innaccurate equipment and records only collected ina few places
Modern records are more reliable as they have data logging
equipment
Allows more numbers of readings to be taken from many places
around the world
Pollen in peat bogs can give an indication to climate in regions. Pollen grains
are resistant to decay. The species of pollen within peat can determine climate within
different time periods.
Peat forms when plant material dies but does not decompose
Lower layers are the oldest
Measuring traces of carbon-14 can be used to establish age of
layers
Dendrochronology is the study of tree rings. Each year, an outer ring is formed.
The thickness of the ring can give an indication as to the climate present in a certain
time period and amount of growth (warmer = thicker ring)
19 Describe that data can be extrapolated to make predictions, that these are used
in models of future global warming, and that these models have limitations.
Climate change models can be used to make predictions about future global
warming

 This can be formed from extrapolation of data (prediction of trends of data for
the future)
Problem is that there is not enough true understanding of the factors and
variables surrounding global warming, so not all conclusions can be fully valid
Another problem is the further we predict into the future, the more
uncertainties arise
20 Discuss the way in which scientific conclusions about controversial issues, such
as what actions should be taken to reduce global warming or the degree to which
humans are affecting global warming, can sometimes depend on who is reaching
the conclusions.
Degree to how humans are affecting global warming
Increase in combustion of fossil fuels (e.g. coal, oil, petroleum, natural gas)
increased CO2 concentration (from vehicle usage in farming)
Destruction of carbon sinks (e.g deforestation of trees which release CO2 back
into the atmosphere when burnt)
Fracking (Extraction of shale gas) increases methane emissions as more
decaying waste gives off CO2 (also by natural excretion from animals which give off
methane as a waste gas)
Thawing of permafrost (frozen ground) releases more methane into the
atmosphere as temperature increases
Actions to reduce global warming
Reduce CO2 concentration
Biofuels - produced from plants which was recently living.
Replace fossil fuels. Although produces CO2, there is no net increase in CO2
concentration (carbon neutral)
Reforestation - Planting of new trees in existing forests that
have been depleted. More CO2 is absorbed, so less CO2 is kept in the
atmosphere and is used for photosynthesis instead.
Building more wind turbines which would produce electricity without increasing
the CO2 concentration
In favour of strategies
Governments can fund the farming of crops for biofuels (Farmers)
Price of biofuels is lower than oil based fuels
Sales of wind turbine companies would increase
Wind turbines do not increase the CO2 concentration
Against strategies
Forests will be cleared to create land for farming of crops for biofuels

Using farmland to grow crops for biofuels can lead to food shortages
Wind turbines have killed many birds
Wind turbines ruin the landscape.

Why scientific conclusions about global warming depend on who is reaching the
conclusions
Conclusions made are judged on
Reliability of data
Evidence
No direct evidence to show a causal link between
variables
Consideration of other limiting factors
Evidence is past from being used
Past evidence is not an indicator of future events
Bias
Scientists may be biased
May be employed by a company with vested
interest
Conclusions arent objective and are based off an
opinion)
21. Describe how evolution (a change in allele frequency) can come about through
gene mutation and natural selection.

Evolution - A change in the allele frequency over time

Conditions for evolution
Variation - Must be differences between the individuals in a
population
Heredity - Differences between organisms must be heritable
Means of selection - Must be a mechanism or pressure that
favours some variables for the next generation over others.
How genetic variation can arise
Gene mutations:
Deletion or addition of a nucleotide
Deletion or translocation of part of a chromosome
Aneuploidy - Loss or gain of a single chromosome
Polyploidy - Addition of a whole chromosome
Meiosis
Independent assortment
Crossing over
Natural Selection
There is a struggle for existence more offspring are
made than survive

 Selection pressure Condition that favours organisms with

alleles that code for advantageous traits

Types of selection:
Disruptive - Selection pressure towards both
extremes, creating 2 modal values
Stabilising - Selection pressure towards centre,
this increases the number of individuals at the modal value
Directional - Selection pressure moves towards
the one extreme moves the mode in this direction
Humanity as a selection pressure
Use of antibiotics [bacteria that carry allele for
resistance will survive and reproduce]
Produces a resistant population
Artificial selection Humans decide which members of a
population will breed
Allows desirable alleles to be maintained in the
gene pool of a population
Used by farmers to produce animals, and plants
with a high yield
Can lead to inbreeding low genetic
diversity
This can increase risk of disease
22. Explain how reproductive isolation can lead to speciation.
Speciation - The formation of a new species over time
Gene pool - Complete range of alleles in a population of a species.
Genetic drift - Change in allele frequency over time.
This occurs when gene flow between a population has been stopped where it
once previously existed
Requires 2 populations of the same species to be reproductively isolated
Reproductive isolation - Change in allele frequency causes changes in
phenotype, therefore separate populations can no longer breed together to produce
fertile offspring

Allopatric speciation
Populations are geographically isolated
Populations are each exposed to different conditions in their
environments
Become adapted to their environments (by natural
selection) giving rise to different phenotypes
Mutations and change in allele frequencies
Will become reproductively isolated and populations will no
longer produce fertile offspring together

Sympatric speciation
Occurs in same place (no geographical isolation)
Species exist in breeding populations (demes)
Demes are reproductively isolated due to changes in the
reproductive mechanism
Also one population may carry beneficial alleles to exploit and
be adapted to a microhabitat
Causes of Reproductive isolation:
Pre zygotic barriers
Habitat - Select diff. habitats, therefore do not
meet
Temporal - Have different mating or flowering
periods
Behavioural - Have different mating calls,
therefore cannot recognise members of other population as mating
partners
Mechanical - Anatomical differences in genitalia
prevent fertilization
Gametic - Female gamete fails to meet male
gamete
Post zygotic barriers
Low hybrid zygote vigour - Zygote fails to develop
properly and dies during embryonic development/ offspring has severe
abnormalities
Hybrid invibility- Offspring fails to thrive and grow
properly
Hybrid infertility - Offspring appears healthy but
infertile

23 Describe the role of the scientific community in validating new evidence

(including molecular biology, eg DNA, proteomics) supporting the accepted scientific
theory of evolution (scientific journals, the peer review process, scientific
conferences).

Anatomical Evidence:
Living species: Darwin's Finches and their anatomical
differences (beaks) which were suitable for their niche.
Fossils: Some show transition between animal groups. Often a
missing link is based off of anatomical features.

 Comparative anatomy: Limbs of living and extinct species show

similarities anatomically. Suggests organisms are likely to share a constant
ancestor.
Artificial selection: Selective breeding (e.g the domestication of
animals by humans) Humans provided selection pressures showing animals can
undergo dramatic changes.

Molecular evidence:
DNA genetic code is universal
Respiration and ATP universal molecule for energy
storage
All have DNA and RNA
Proteins in all organisms, formed from the same 20 amino acids
All have phospholipid membranes
Similar metabolic pathways

Proteomics
Study of similarities in protein size and shape
Amino acid sequence is coded by the DNA sequence
Look at similarities in DNA sequences
Look at similarities in amino acid sequences
Organisms that have undergone speciation recently will have
more similarities
Genomics
Study of similarities in DNA base sequences in the genes
Analysed by DNA hybridisation/profiling/molecular clocks
Distantly related species will show less similarities due to the
high number of mutations occurring over time

Validating new evidence

Scientific journals are used to share theories
These can then be validated by peer review for validity
Replicating the experiment to test for reliability and validity
Scientific questions allow theory to be discussed
This retains validity

Reliability - Repeatability; to what extent can the same results be produced

again
Validity - To what extent have other factors been taken into account and
controlled
Precision - Results show minimal error
Accuracy - Results are close to true value