Unit 4 Flashcards
The reaction of photosynthesis consists of:
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
what at ATP known for
known as the universal energy currency and it diffuses within cells to where it is needed. it is an immediate supply of energy for biological processes
function of ATP
is used to transfer and supply energy within cells
what is ATP made of
It is a phosphorylated nucleotide
ATP contains adenine, a ribose sugar, and three phosphates molecules. Removal of one phosphate creates ADP, and removal of two phosphates creates AMP.
how is ATP produced
ATP is produced by the addition of inorganic phosphate (Pi), a type of phosphate group, to adenosine diphosphate, or ADP in photophosphorylation, energy is needed.
How is the energy released
The hydrolysis, or breakdown, of ATP releases an inorganic phosphate as well as a small amount of energy which can be used by the cell.
The hydrolysis of ATP is catalysed by the enzyme ATPase
The ADP and inorganic phosphate produced by the hydrolysis of ATP can be recycled to make more ATP
what stages does photosynthesis take place
The light-dependent reactions, which rely on light directly
The light-independent reactions, which do not use light directly, though do rely on the products of the light-dependent reactions
where does photosynthesis take place
Both these sets of reactions take place within the chloroplast
The light-dependent reactions take place across the thylakoid membrane
The light-independent reactions take place in the stroma
why is light needed in the light dependent reactions
enables the splitting of water molecules in a reaction known as photolysis
it excites the electrons into higher energy levels in order to allow then to go into an ETC
what does photolysis produce
2 hydrogen ions (2H+), also known as protons
2 electrons (2e-)
One atom of oxygen (O)
The hydrogen ions and electrons are used during the light-dependent reactions while the oxygen is given off as a waste product
what is NADP
NADP is a type of molecule called a coenzyme; its role is to transfer hydrogen from one molecule to another
what happens to reduced NADP and ATP after the light dependent reactions
are transferred to the light-independent reactions within the chloroplast
what does non-cyclic photophosphorylation produce
This produces both ATP and reduced NADP
what does cyclic photophosphorylation produce
his produces ATP only
what does Both cyclic and non-cyclic photophosphorylation involve
A series of membrane proteins which together make up the electron transport chain and Chemiosmosis
what is the ETC
Electrons pass from one protein to another along the electron transport chain, releasing energy as they do so
what is chemiosmosis
The energy released as electrons pass down the electron transport chain is used to produce ATP
what happens in non-cyclic photophosphorylation
Light energy hits photosystem II in the thylakoid membrane
Two electrons gain energy and are excited to a higher energy level
The excited electrons leave the photosystem and pass to the the electron transport chain
As the excited electrons leave photosystem II they are replaced by electrons from the photolysis of water
The electrons pass down the electron transport chain
Energy is released as the electrons pass down the chain which enables chemiosmosis to occur
H+ ions are actively pumped from a low concentration in the stroma to a high concentration in the thylakoid space, generating a concentration gradient across the thylakoid membrane
H+ ions diffuse back across the thylakoid membrane into the stroma via ATP synthase enzymes embedded in the membrane
The movement of H+ ions causes the ATP synthase enzyme to catalyse the production of ATP
At the end of the electron transport chain the electrons from photosystem II are passed to photosystem I
Light energy also hits photosystem I, exciting another pair of electrons which leave the photosystem
The excited electrons from photosystem I also pass along an electron transport chain
These electrons combine with hydrogen ions from the photolysis of water and the coenzyme NADP to form reduced NADP
what happens in cyclic photophosphorylation
Light hits photosystem I
Electrons are excited to a higher energy level and leave the photosystem
The excited electrons pass along the electron transport chain, releasing energy as they do so
The energy released as the electrons pass down the electron transport chain provides energy to drive the process of chemiosmosis
H+ ions are actively pumped from a low concentration in the stroma to a high concentration in the thylakoid space, generating a concentration gradient across the thylakoid membrane
H+ ions diffuse back across the thylakoid membrane into the stroma via ATP synthase enzymes embedded in the membrane
The movement of H+ ions cause the ATP synthase enzyme to catalyse the production of ATP
At the end of the electron transport chain the electrons rejoin photosystem I in a complete cycle
The ATP produced enters the light-independent reaction
what is the Calvin cycle
The light-independent reactions of photosynthesis
what does photosynthesis allow the plant to produce
complex organic molecules such as
Starch for storage
Sucrose for transport
Cellulose for making cell walls
what does the light-independent reaction need
require ATP and reduced NADP from the light-dependent reactions
what are the 3 main steps of the calcin cycle
Carbon dioxide is combined with ribulose bisphosphate (RuBP), a 5-carbon (5C) compound; this yields two molecules of glycerate 3-phosphate (GP), a 3-carbon (3C) compound
GP is reduced to glyceraldehyde 3-phosphate (GALP), another 3C compound, in a reaction involving reduced NADP and ATP
RuBP is regenerated from GALP in reactions that use ATP
what allows the reaction of RuBP and CO2
Carbon dioxide combines with a 5C sugar known as RuBP in a reaction catalysed by the enzyme rubisco
what does the reaction between RuBP and CO2 produce
The resulting 6-carbon (6C) compound is unstable and splits in two
This results in two molecules of a 3C compound known as glycerate 3-phosphate (GP)
What happens after two GP molecules have been created in the Calvin cycle
Energy from ATP and hydrogen from reduced NADP are used to reduce the two 3C molecules of GP to two 3C molecules known as GALP
what is GALP used for
Some of the carbons in GALP go towards the production of useful organic molecules such as glucose, while the rest remain in the Calvin cycle to allow the regeneration of RuBP
Two molecules of GALP contain six carbon atoms
how does the regeneration of RuBP take place
Five sixths of the GALP molecules are used to regenerate RuBP
This process requires ATP
what are the intermediate products of the calvin cycle used for
Intermediate molecules of the Calvin cycle, such as (GALP), are used to produce hexose sugars e.g. glucose (which react to make sucrose, cellulose…) , glycerol can be used for building lipid molecules, fatty acids, nucleic acids (created by the combination of this product with P of soil), acetyl coenzyme A, amino acids (created by the combination of this product with NO3 of soil),
Many of the molecules produced are used to build new plant biomass
what are the intermediate products of the calvin cycle used for
Intermediate molecules of the Calvin cycle, such as (GALP), are used to produce hexose sugars e.g. glucose (which react to make sucrose, cellulose…) , glycerol can be used for building lipid molecules, fatty acids, nucleic acids (created by the combination of this product with P of soil), acetyl coenzyme A, amino acids (created by the combination of this product with NO3 of soil),
Many of the molecules produced are used to build new plant biomass
function of the chemicals produced from the intermediate products of the calvin cycle (generally)
Many of the molecules produced are used to build new plant biomass
how is the reaction of CO2 and RuBP called
carbon fixation
definition of absorption spectrum
a graph showing the amount of light absorbed by a pigment against the wavelenght of the light
definition of action spectrum
a graph demonstrating the rate of photosynthesis against the wavelength of light
function of the chloroplasts
Chloroplasts are the organelles in plant cells where photosynthesis occurs
how many membranes does a chloroplast have
Each chloroplast is surrounded by a double-membrane known as the chloroplast envelope
Each of the envelope membranes is a phospholipid bilayer
what is the stroma
with a cytoplasm-like fluid found in chloroplasts
what does the stroma contain
The stroma contains enzymes and sugars, as well as ribosomes and chloroplast DNA
If the chloroplast has been photosynthesising there may be starch grains or lipid droplets in the stroma
what is the special set of membranes found in the stroma
This membrane system consists of a series of flattened fluid-filled sacs known as thylakoids, each surrounded by a thylakoid membrane
Thylakoids stack up to form structures known as grana (singular granum)
Grana are connected by membranous channels called lamellae (singular lamella), which ensure the stacks of sacs are connected but distanced from each other
what does the thylakoid membrane contain that is essential for photosynthesis
ATP synthase enzymes
Proteins called photosystems that contain photosynthetic pigments such as chlorophyll a, chlorophyll b, and carotene
function of chloroplast envelope
The double membrane encloses the chloroplast, keeping all of the components needed for photosynthesis close to each other
The transport proteins present in the inner membrane control the flow of molecules between the stroma and cytoplasm
function of stroma
The gel-like fluid contains enzymes that catalyse the reactions of photosynthesis
function of DNA
The chloroplast DNA contains genes that code for some of the proteins used in photosynthesis
function of ribosomes
Ribosomes enable the translation of proteins coded by the chloroplast DNA
function of thylakoid membranes
There is a space between the two thylakoid membranes known as the thylakoid space, in which conditions can differ from the stroma e.g. a proton gradient can be established between the thylakoid space and the stroma
The space has a very small volume so a proton gradient can develop very quickly
function of grana
The grana create a large surface area, maximising the number of photosystems and allowing maximum light absorption
Grana also provide more membrane area for proteins such as electron carriers and ATP synthase enzymes, which together enable the production of ATP
function of photosystems
There are two types of photosystems; photosystem I and photosystem II, containing different combinations of photosynthetic pigments such as chlorophyll a, chlorophyll b, and carotene
Each photosystem absorbs light of a different wavelength, maximising light absorption e.g. photosystem I absorbs light at a wavelength of 700 nm while photosystem II absorbs light at a wavelength of 680 nm
what are the different pigment groups fround in chloroplasts
Chlorophylls and Carotenoids
what colour of the light spectrum does chlorophylls absorb
wavelengths in the blue-violet and red regions of the light spectrum, reflecting green light and appearing green in colour
what colour of the light spectrum does carotenoids absorb
wavelengths of light mainly in the blue-violet region of the spectrum, reflecting yellow and orange light
Carotenoids often remain in leaves after the breakdown of chlorophyll in the autumn, giving some leaves their yellow, orange, and red autumn colours
how can chloroplast pigments be separated
Chromatography can be used to separate and identify chloroplast pigments that have been extracted from a leaf
how can chloroplast pigments be identified after a chromatography
Different components within a mixture travel through materials at different speeds due to their size or charge
This causes different components to separate
An Rf value can be calculated for each component of the mixture on the basis of its rate of movement
what is primary productivity
The rate at which producers convert light energy into chemical energy
what is gross primary productivity (GPP)
the rate at which chemical energy is converted into carbohydrates during photosynthesis
how is NPP connected to GPP
Net primary productivity, or NPP, is the GPP minus plant respiratory losses
Of the total energy stored in glucose during photosynthesis, 90 % will be released from glucose to create ATP for the plant during respiration
90 % of the energy originally converted by the plant will therefore not be stored as new plant biomass and will not be available to be passed on to herbivores, also known as primary consumers
equation to calculate NPP
NPP= GPP - R
units for NPP
NPP is expressed in units of energy per unit area or volume per unit time e.g.
Using area: J m–2 yr-1 (joules per square metre per year)
Using volume: J m–3 yr-1 (joules per cubic metre per year)
Volume would be used when calculating NPP in aquatic habitats
rearragement of equation to calculate GPP or R with NPP
GPP = NPP + R
R = GPP - NPP
definition of population
a group of organisms of the same species, living and breeding together in a habitat
definition of community
all the populations of all the different species of organisms living in a habitat at any one time
definition of habitat
the place where an organism lives
definition of ecosystem
an environment including all the living organisms interacting within it, the cycling of nutrients and the physical and chemical environment in which the organisms are living
what affects the number and sitribution of organisms in a habitat
biotic and abiotic factors
what is a biotic factor
are living factors that influence populations within their community; biotic factors come about as a result of the activity of other organisms
examples of biotic factors
Predation
Food availability
Intraspecific competition, arising when individuals of the same species compete for resources
Interspecific competition, arising when individuals of different species compete for resources
Cooperation between organisms
Parasitism
Disease
examples of abiotic factors
Light intensity and wavelength
Temperature
Turbidity, or cloudiness, of water
Humidity
Soil or water pH
Soil or water salinity
Soil composition
Oxygen or Carbon dioxide concentration
what are abiotic factors
are non-living factors that influence populations within their community
what does the niche include
What it eats
Which other species depend on it for food
What time of day a species is active
Exactly where in a habitat a species lives
Exactly where in a habitat a species feeds
important characteristics to take into account about niches
No two species can fill the same niche within a habitat
The niche filled by a species determines its abundance within a habitat
The niche filled by a species determines its distribution
why cant two species fill the same niche within a habitat
the two species will be in direct competition with each other for resources, and one of the two species will out-compete the other, causing it to die out in that particular habitat
why the niche determines the abundance of that specie
If two species occupy a similar niche within a habitat they will be competing with each other, so their populations will be smaller, and their abundance will therefore be lower
why the niche determines the distribution of that specie
Species can only survive in habitats to which they are well adapted; if they are not well suited to a habitat’s biotic and abiotic factors then they will move to a more suitable habitat and their distribution will change
what is succession
The process of ecosystem change over time
what is primary succession
is the process that occurs when newly formed or newly exposed land is inhabited by an increasing number of species
how can newly formed land be created
The magma from erupting volcanoes cooling and forming new rock surfaces or new rocky islands in the sea
how can newly exposed land form
A landslide that exposes bare rock
A glacier that retreats to reveal bare rock
what is colonisation
The arrival of organisms on bare land is known as colonisation, and the bare land is said to be colonised
where can succession occur
any type of bare land, including sand dunes at the edge of the ocean, and on exposed rock
steps of primary succession
Seeds and spores that are carried by the wind land on exposed rock and begin to grow
The first species to colonise the new land are pioneer species
Pioneer species can germinate easily and withstand harsh conditions such as low nutrient and water availability
As pioneer species die and decompose, the dead organic matter forms soil
Seeds of small plants and grasses land on this soil and begin to grow
The plants at this early stage of succession are adapted to survive in shallow, nutrient-poor soils
The roots of these small plants form a network that helps to hold the soil in place and prevent it from being washed away
As these small plants die and decompose, the soil becomes deeper and more nutrient-rich
Larger plants and shrubs, as well as small trees can now begin to grow
These larger plants and small trees also require more water, which can be stored in deeper soils
Over time the soil becomes sufficiently deep, contains enough nutrients, and can hold enough water to support the growth of large trees
The final species to colonise the new land become the dominant species of the now complex ecosystem
The final community formed, containing all the different plant and animal species that have now colonised the land, is the climax community
A climax community is not always the most biodiverse stage of succession, but it is a stable community
difference between secondary and primary succession
secondary succession takes place on previously occupied land e.g. after a wild fire or deforestation
Secondary succession is very similar to primary succession except that soil is already present so the process begins at a later stage
how can humans prevent succession
stops a climax community from developing
Regular mowing prevents woody plants from establishing themselves in a lawn
The grazing activity of livestock such as sheep and cattle prevent new plants from establishing
what are plagioclimax
Climax communities that develop as a result of human intervention; these communities are stable but would not have occurred without human intervention, e.g. heathland
types of evidence for climate change
Records of atmospheric carbon dioxide levels
Records of average global temperatures
Records of changing plant communities gained from sampling of pollen grains preserved in peat over time
Records of tree growth gained by analysing the rings in the trunks of trees; known as dendrochronology
what forms peat
Under waterlogged and acidic conditions partly decomposed dead plant matter accumulates and becomes compacted under its own weight over time; this compacted, partially decomposed plant matter
where is peat found
The place where peat accumulates is known as a peat bog, or peatland
why is peat analysed
Peat builds up in layers, meaning that layers of peat at the top of a bog are recently formed and the peat become older as you dig down into a bog
Peat cores can be taken from a bog and the layers can be analysed to assess the pollen grains that have become trapped in the peat
why is studying pollen in peat bogs useful?
the pollen grains of each plant species are unique to that plant, the plant species that were growing around the bog at different points in time can be identified
Different plant species grow under different climatic conditions, so the plants present at different times can be used a measure of the climate at that time
what is looked at when studying tree rings in dendrochronology
Light coloured rings are produced by fast growth during warmer spring and summer months and dark coloured rings form as a result of slow autumn growth, meaning that one light ring and one dark ring together represent a full year’s growth in a tree
Trees grow faster when conditions are warmer, so the rings that form during warm years are wider than the rings that form during cool years
why do we study tree rings
Analysis of the width of tree rings can provide a measure of climate during each year of growth
what is a greenhouse gas
a gas that absorbs this re-radiated radiation, trapping it in the earth’s atmosphere so that it is not lost to space
one cause of anthropogenic climate change: what releases CO2
In addition to the burning of fossil fuels, carbon dioxide is also released into the atmosphere when natural stores of carbon are damaged or destroyed by human activities
These carbon stores are known as carbon sinks
Carbon sinks include trees, soils, peat bogs, and the oceans
Deforestation, soil degradation, peat harvesting, and ocean warming all contribute to the addition of carbon dioxide to the atmosphere
one cause of anthropogenic climate change: what releases Methane
Methane is released from the guts of ruminant mammals such as cattle
Landfill sites release methane when organic matter such as food waste decomposes
Extraction of fossil fuels from underground releases methane
Anaerobic bacteria in waterlogged rice paddy fields release methane
what are the events in the carbon cycle
Carbon is present in the atmosphere in the form of carbon dioxide
Carbon dioxide is removed from the atmosphere by producers during photosynthesis and incorporate carbon into their biomass in the form of carbohydrates and other biological molecules
Carbon is transferred to and between consumers as a result of feeding
Carbon is transferred back into the atmosphere by both plants and animals as a result of respiration as it releases co2 as a product
Carbon dioxide can also be removed from the atmosphere by dissolving in the oceans
Dissolved carbon can be taken in by marine plants when they photosynthesise or by other marine organisms as they build calcium carbonate exoskeletons
When living organisms die their tissues are broken down by decomposers such as bacteria and fungi
When these organisms respire, they too release carbon dioxide back into the atmosphere
Any living tissue that is not fully decomposed can go towards the formation of peat or fossil fuels over millions of years; carbon can be stored in these sinks for long periods
The combustion of peat and fossil fuels releases carbon dioxide back into the atmosphere
The combustion of biomass such as wood also returns carbon to the atmosphere
how can the carbon cycle be used to prevent further increases in atmospheric carbon dioxide
Reducing the combustion of fossil fuels
Reducing the combustion of biomass
Reducing disturbance of carbon pools such as soils and peat bogs
Increasing rates of photosynthesis by planting trees
how can we make predictions about future climate change
Extrapolated data can be used to produce models that show how the climate may change in the future
what can extrapolated climate change data be used for
Building flood defences
Funding scientific research into climate change technologies
Reduce the burning of fossil fuels
Increase the use of renewable energy sources such as solar and wind energy
Reduce meat consumption
what are the limitations of Climate Change Prediction Models
The IPCC has produced models based on several emissions scenarios, and we do not know which of these scenarios is most likely
We do not know whether future technologies will be successful at removing greenhouse gases from the atmosphere
It is unknown exactly how atmospheric gas concentrations might affect global temperatures
Global climate patterns are complex and therefore predictions are difficult
It is possible that a certain tipping point in global temperatures could lead to a sudden acceleration in global warming
We don’t know exactly how factors other than human activities may affect climate in the future
impacts on climate patterns of Increased atmospheric warming
Weather events becoming more extreme
Changes to ocean currents leading to altered local climates
Warmer air can hold more moisture, leading to changes in patterns of rainfall; more, heavier rainfall in some places could lead to reduced rainfall in other locations
impact on animals and plants of increased atmospheric warming
Warming climates cause animals to move towards the poles or to higher altitudes
these species may not be able to compete with, or may even out-compete, the species already present in these habitats, with either result leading to decreased biodiversity
Some species, such as plant species, may not be able to move or change their distribution fast enough to adapt to changing temperatures and may become extinct as a result
impact on water availability iof increased atmospheric warming
Changes to rainfall patterns can be devastating to species that rely on seasonal rains for their survival
Some species may no longer be able to survive in their habitat due to a lack of rainfall; such species may migrate to a new habitat or may become extinct
impact on seasonal changes of increased atmospheric warming
Plant species are producing flowers earlier in the year
Animals are producing young earlier in the year
Bird migratory patterns may lose their synchronisation with their habitats, leading to a change in migration patterns
impact on Polar ice and glaciers retreating of increased atmospheric warming
The loss of glacier ice from mountain ranges may affect the water supplies of many people and surrounding wildlife
impact on Sea levels rising of increased atmospheric warming
people and animals at risk of being flooded out of their homes
Sea levels are rising due to the expansion of warmer water and due to melting polar ice
what is the optimum temperature of enzymes
Enzymes have a specific optimum temperature
This is the temperature at which they catalyse a reaction at the maximum rate
how can low temperatures affect enzyme activity
prevent reactions from proceeding or slow them down
Molecules move relatively slowly as they have less kinetic energy
Less kinetic energy results in a lower frequency of successful collisions between substrate molecules and the active sites of the enzymes which leads to less frequent enzyme-substrate complex formation
Substrates and enzymes also collide with less energy, making it less likely for bonds to be formed or broken
how can high temperatures affect enzyme activity (without denaturing)
reactions to speed up
Molecules move more quickly as they have more kinetic energy
Increased kinetic energy results in a higher frequency of successful collisions between substrate molecules and the active sites of the enzymes which leads to more frequent enzyme-substrate complex formation
Substrates and enzymes also collide with more energy, making it more likely for bonds to be formed or broken
why if temperatures continue to increase past a certain point, the rate at which an enzyme catalyses a reaction drops sharply?
the enzymes begin to denature
The increased kinetic energy and vibration of an enzyme puts a strain on its bonds, eventually causing the weaker hydrogen and ionic bonds that hold the enzyme molecule in its precise shape to start to break
The breaking of bonds causes the tertiary structure of the enzyme to change
The active site is permanently damaged and its shape is no longer complementary to the substrate, preventing the substrate from binding
Denaturation has occurred if the substrate can no longer bind
what is the temperature coefficient
The temperature coefficient, represented by Q10, calculates the increase in rate of reaction when the temperature is increased by 10 degreeC
Q10 = rate at higher temperature divided byrate at lower temperature
how can chemical reactions in living organisms be affected by temperature and therefore enzyme activity
Some chemical reactions take place faster at higher temperatures
Some chemical reactions are slowed down at higher temperatures
The sex of the young inside the egg of some species is determined by temperature, so increasing temperatures can affect the sex ratios in a species
Species may have to change their distribution in response to changing temperatures in order to survive
example of chemical reactions in living organisms taking place faster at higher temperatures
Photosynthesis is essential for converting carbon dioxide into carbohydrates, the process which produces food for producers and other organisms higher up the food chain; it relies on the function of proteins in the electron transport chain and that of enzymes such as rubisco
example of chemical reactions which are slowed down at higher temperatures
At high temperatures plants carry out a reaction called photorespiration at a faster rate; this reaction uses the enzyme rubisco and so slows down photosynthesis
This can reduce crop yields as temperatures rise
Some fish eggs have been shown to develop more slowly at higher temperatures
Many species’ successful egg development is dependent on temperature, with impacts such as
Extreme temperature fluctuations can reduce hatching rates in some invertebrates
example of Species having to change their distribution in response to changing temperatures in order to survive
Species may migrate to higher altitudes or further from the equator to find cooler temperatures
what is evolution
changes in the heritable characteristics of organisms over generations
how can heritable characteristics contribute to the evolution of a species
Heritable characteristics are determined by the alleles of genes that are present in an individual
Alleles may change as a result of random mutation, causing them to become more or less advantageous
Heritable characteristics that are advantageous are more likely to be passed on to offspring, leading to a gradual change in a species over time
This is the process of natural selection
what is natural selection
the process by which organisms that are better adapted to their environment survive, reproduce, and pass on their advantageous alleles, causing advantageous characteristics to increase in frequency within a population
what is neccessary for natural selection to take place
Natural selection can only take place if variation is present
where does variation within a specie come from
Variation results from small differences in DNA base sequences between individual organisms within a population
Sources of variation include
Mutation
Meiosis
Random fertilisation during sexual reproduction
what are selection pressures
Environmental factors that influence survival chances are said to act as selection pressures
what are non-heritable characteristics
those acquired during the lifetime of an organism
main events that allow natural selection to occur
Variation exists between individuals in a population
In any habitat there are environmental factors that affect survival chances
In any population, due to the variation present, some individuals will have characteristics that make them better adapted for survival in the face of any selection pressures (This is sometimes described as ‘survival of the fittest’)
Individuals that are well adapted and survive into adulthood are more likely to find a mate and reproduce, producing many offspring
This means that they are more likely to pass on the alleles that code for these advantageous characteristics to their offspring
The number of individuals in a population with a particular favourable characteristic will increase over time; the characteristic is said to increase in frequency
Eventually this favourable characteristic will become the most common of its kind in the population; the population can be said to have adapted to its environment by the process of natural selection
what is speciation
the development of new species from pre-existing species over time
what needs to happen for speciation to occur
two populations of the same species must be isolated from each other in some way
When this happens, there can no longer be an exchange of genes between the two populations
The exchange of genes is sometimes known as gene flow
how can isolation of populations occur
Geographical isolation
This leads to a type of speciation known as allopatric speciation
Random mutations that prevent them from interbreeding with each other
This leads to a type of speciation known as sympatric speciation
overall events for speciation
Populations that are isolated from each other may face different selection pressures in their environment
The different environmental conditions for the two populations might mean that different alleles are advantageous, so different alleles are more likely to be passed on and become more frequent in each population; this is the process of natural selection
The allele frequencies in the two populations change over time
Note that a process known as genetic drift can also affect allele frequencies
Over time the two populations may begin to differ physiologically, behaviourally and morphologically to such an extent that they can no longer interbreed to produce fertile offspring; speciation has occurred
when does allopatric speciation occur
Allopatric speciation occurs when populations of a species become separated from each other by geographical barriers
The barrier could be natural
It can also be man-made
events in allopatric speciation
creates two populations of the same species between which no gene flow is taking place
Allele frequencies in the gene pools of the two populations may change in different ways due to
Different selection pressures acting on them
The accumulation of random changes resulting from genetic drift
Changing allele frequencies will lead to changes in the phenotypes of the two populations
If enough allele frequency differences arise between the two populations, then they will eventually no longer be able to breed with each other and produce fertile offspring, and can be said to be separate species
when does sympatric speciation occur
Isolation occurs when random changes in the alleles and therefore phenotypes of some individuals in a population prevent them from successfully breeding with other individuals in the population. such as:
Seasonal changes
Mechanical changes
Behavioural changes
events in sympatric speciation
The populations may still live in the same habitat but they are isolated from each other in the sense that they do not interbreed
The lack of gene flow between the two populations means that allele frequencies in the gene pools of the two populations may change in different ways
Changing allele frequencies will lead to changes in the phenotypes of the two populations
If enough allele frequency differences arise between the two populations, then they will eventually no longer be able to breed with each other and produce fertile offspring, and can be said to be separate species
factors to take into account when evaluating climate change claims
There is a great deal of scientific evidence that has been tested and checked by other scientists that supports the hypothesis that humans burning fossil fuels causes climate change
Climate is highly complex
People may have a personal interest; some are especially passionate about the environment, while others depend financially on fossil fuels
It is important that we are aware of the personal biases of those making claims about the causes of climate change
Examples of Sustainable Conservation
Reducing carbon emissions
Biofuels
Other renewable sources
Increasing carbon removal
how can we reduce carbon emissions
limiting the rate at which fossil fuels are burned by
Burning biofuels instead of fossil fuels
The use of other renewable energy resources
advantages of biofuels
Biofuels are often cheaper than oil
It is argued that biofuels are ‘carbon neutral’ meaning that they only release carbon that was recently removed from the atmosphere when the plants were alive
They do not release carbon that has been stored away for millions of years as with fossil fuels
Biofuels are a renewable source of energy, i.e. they can be regrown quickly
disadvantages of biofuels
They do still release carbon dioxide into the atmosphere
The vast amounts of land required to grow biofuels could otherwise have been used for food production
Creating land for biofuel growth often involves the loss of other types of habitats e.g. rainforest; this is bad for biodiversity
Cutting down mature trees to create land for biofuel growth reduces the removal of carbon from the atmosphere by photosynthesis
advantages of other renewable sources
These kinds of technologies are advancing quickly and are becoming cheaper and more efficient to use
No carbon dioxide is released when these technologies are used to generate electricity
disadvantages of other renewable sources
Geothermal energy can only be used when there is volcanic activity close to the earth’s surface
Solar energy depends on sunshine hours
Wind energy depends on wind speeds and some conservationists are concerned about the impact of wind turbines on birds and bats
Some are also concerned about the visual impact of wind turbines on the landscape
Tidal energy can only be generated near the coast
how can humans increase the global rates of photosynthesis?
Stopping the destruction of forests by deforestation
Planting trees, also known as reforestation
If trees are allowed to grow to maturity, they can store huge amounts of carbon in their biomass
what do microorganisms be provided with to grow
Nutrients
Oxygen
Note that anaerobic microorganisms would require the absence of oxygen
Optimum pH
Favourable temperature
why should microorganisms be cultured with great care
There is always the risk that a mutation could lead to the formation of pathogenic strains
Pathogenic bacteria from the environment could contaminate the bacterial culture being investigated
what should you remember to do when culturing microorganisms
Follow health and safety precautions
Ensure that all equipment are sterilised before culturing the bacteria
Sterilising involves killing microorganisms, e.g. by heating to a high temperature or the use of antimicrobial chemicals
Keep the culture in the laboratory
Seal cultures in a plastic bag and sterilise at high temperature and pressure before disposal
Steps to take in order to culture microorganisms
Obtain a supply of the type of microorganism to be cultured
Provide them with the correct type of nutrients to facilitate growth
A nutrient growth medium in the form of a liquid culture or a solid nutrient agar
Ensure that the nutrient medium is kept under sterile conditions until use
By adjusting the type of nutrients in the medium, conditions will be created for the optimal growth of a certain type of microorganism; this is known as a selective medium
Microorganisms are introduced to a growth medium using inoculation with a sterilised inoculation loop
Inoculation can be used to transfer microorganisms between media
The new medium should be sealed or covered to avoid contamination from microorganisms in the air; if growing aerobic microorganisms any seal or cover should not be airtight
Flasks can be sealed with a sterile cotton wool stopper
Petri dishes can be covered with a lid
Label the medium clearly and incubate at around 20 °C to prevent the growth of pathogenic microorganisms
how can you culture a single type of microorganism
In order to grow a single type of microorganism, or a pure culture, the specific microorganism must be isolated
This can be done by using knowledge about the needs of the microorganism to be cultured or those of microorganisms that may contaminate the culture
Being able to isolate pathogenic microorganisms is useful in the diagnosis and treatment of diseases
methods that can be used to count microorganisms when cultured
Cell counts
Dilution plating
Measuring area and mass
Optical methods
steps to take when cell counting with microscope and haemocytometer
A nutrient broth is diluted with an equal volume of trypan blue
The chamber of the haemocytometer is filled with the stained nutrient broth
The number of living cells in the four corner squares of the grid are counted
Each corner square consists of 16 smaller squares
Consistency needs to be used when deciding whether to count cells that are on the lines that border the corner squares
The mean number of cells from the four corner squares can be calculated
why is trypan blue dye used in cell counting
This is a dye that will stain dead cells blue
It enables the investigator to only count the living cells
why is the haemocytometer calibrated
to allow the calculation of the number of cells in a known volume of broth
Because the haemocytometer chamber can hold exactly 0.1 mm3 of liquid, it is possible to estimate of the cell count in 1 ml of nutrient broth using the following calculation
No. of cells per ml nutrient broth = mean cell count x dilution factor x 10 ^4
Multiplying by the dilution factor enables calculation of the bacterial cell count in the original broth rather than the diluted broth
The multiplication by 10 ^4 enables calculation of the bacterial cell count in 1 ml rather than in 0.1 mm3
1 ml = 1 cm3
1 cm3 = 0.1 mm3 x 10 000
10 000 = 1 x 10^4
how can the haemocytometer be used to calculate the bacterial cell count in the original broth rather than the diluted broth
No. of cells per ml nutrient broth = mean cell count x dilution factor x 10 ^4
The multiplication by 10 ^4 enables calculation of the bacterial cell count in 1 ml rather than in 0.1 mm3
1 ml = 1 cm3
1 cm3 = 0.1 mm3 x 10 000
10 000 = 1 x 10^4
what is dilution plating used for
used to determine the total viable cell count in a nutrient broth
The nutrient broth is transferred to agar where the bacteria use nutrients in the agar gel to reproduce
A single cell that lands on agar reproduces by cloning itself, resulting in a mass of identical cells known as a colony
Each microbial colony that grows on agar gel originated with one viable microorganism, so can be counted as one viable cell
why do we dilute the original culture in dilute plating
this reduces the number of cells in the original sample so that individual colonies are visible on an agar plate
how can we determine the total viable cell count in dilution plating
To calculate the total viable cell count, the number of colonies are multiplied by the dilution factor
A mean can be determined if more than one plate is used
how can we use Area and mass of fungi to measure growth of microorganisms
Measuring the diameter of individual areas of the mycelium can be used to determine the growth of fungi
This can be used to compare growth rates in different conditions, e.g. at different temperatures
The larger the mean diameter, the greater the growth of the fungi
Testing the dry mass of fungi is another effective way to measure fungal growth
The higher the mass, the more fungal growth has occurred
how can we measure the diameter of individual areas of the mycelium to determine the growth of fungi
Petri dishes of agar are inoculated with fungal spores and incubated at a suitable temperature
The resulting areas of fungal mycelia are then measured
how can we test the dry mass of fungi to measure fungal growth
A liquid nutrient broth is inoculated with fungal spores
Samples of the nutrient broth are removed at set time intervals
The fungal mycelia are removed by filtering or centrifugation
The material is dried in an oven overnight and its mass measured
The higher the mass, the more fungal growth has occurred
what optical method is used to measure the growth of microorganisms
Turbidimetry
what is turbidimetry
Turbidimetry is a specialised form of colorimetry that can be used as an alternative method to measure the number of cells in a sample
Turbidity is a measure of how cloudy a solution is
More turbid = more cloudy
Less turbid = less cloudy
Colorimetry uses a machine called a colorimeter to shine a beam of light at a sample and measure the amount of light that is either transmitted through or absorbed by the sample
how is turbidimetry used to measure the growth of microorganisms
The higher the number of cells the more turbid the solution becomes
More turbid solutions will absorb more light and allow less light through; this can be measured by a colorimeter
This provides an indirect measure of the number of microorganisms present
A calibration curve can be constructed by measuring the turbidity of a series of control cultures while also counting the cells in each culture using a haemocytometer; the results are plotted in a graph of turbidity against cell count
This curve can then be used to estimate the cell count of unknown samples by measuring their turbidity and then reading their cell count from the graph
process of binary fission
The single, circular DNA molecule undergoes DNA replication
Any plasmids present undergo DNA replication
The parent cell divides into two cells, with the cytoplasm roughly halved between the two daughter cells
The two daughter cells each contain a single copy of the circular DNA molecule and a variable number of plasmids
what is a growth curve
The growth of a bacterial population follows a specific pattern over time
what are 4 phases in the population growth curve of a microorganism population
Lag phase
Exponential phase
Stationary phase
Death phase
what happens in the lag phase in the population growth curve of a microorganism population
The population size increases slowly as the microorganism population adjusts to its new environment and gradually starts to reproduce
what happens in the exponential phase in the population growth curve of a microorganism population
With high availability of nutrients and plenty of space, the population moves into exponential growth; this means that the population doubles with each division
This phase is also known as the log phase
what happens in the stationary phase in the population growth curve of a microorganism population
The population reaches its maximum as it is limited by its environment, e.g. a lack of resources and toxic waste products.
During this phase the number of microorganisms dying equals the number being produced by binary fission and the growth curve levels off
what happens in the death phase in the population growth curve of a microorganism population
Due to lack of nutrients and a build up of toxic waste build up, death rate exceeds rate of reproduction and the population starts to decline
This phase is also known as the decline phase
why are logarithmic scales used in the growth curve of a microorganism population
Logarithmic scales allow for a wide range of values to be displayed on a single graph
To calculate the number of bacteria in a population which formula can be used
kt
Nt = N0 x 2
Nt = the number of organisms at time t
N0 = the number of organisms at time 0
k = the exponential growth rate constant
t = the time for which the colony has been growing
what is the Exponential growth rate constant used for
number of times the population doubles in a given time period
how can you calculate the exponential growth rate constant
log10 (Nt) - log10(N0)
k=_____________________
log10 (2) x t
what are bacteria
single-celled prokaryotes
how do bacteria differ from eukaryotic cells
A cytoplasm that lacks membrane-bound organelles
Ribosomes that are smaller (70 S) than those found in eukaryotic cells (80 S)
No nucleus, instead having a single circular bacterial chromosome that is free in the cytoplasm and is not associated with proteins
A cell wall that contains the glycoprotein murein (peptidoglycan)
structures found only in prokaryotic cells
Loops of DNA known as plasmids
Capsules-It helps to protect bacteria from drying out and from attack by cells of the immune system of the host organism
Flagella (singular flagellum)- Long, tail-like structures that rotate, enabling the prokaryote to move (Some prokaryotes have more than one)
Pili (singular pilus)-Thread-like structures on the surface of some bacteria that enable the bacteria to attach to other cells or surfaces (Involved in gene transfer during sexual reproduction)
A cell membrane that contains folds known as mesosomes; these infolded regions can be the site of respiration
what are viruses
non-cellular infectious particles
what is the structure of viruses
A nucleic acid core
Their genomes are either DNA or RNA, and can be single or double-stranded
A protein coat called a ‘capsid’ made of repeating units known as capsomeres
what is some sturctures that only some viruses have
Some viruses have an outer layer called an envelope formed from the membrane-phospholipids of the cell they were made in
Some contain proteins inside the capsid which perform a variety of functions
Viruses also contain attachment proteins, also known as virus attachment particles, that stick out from the capsid or envelope
how do viruses reproduce
infecting living cells and using the protein-building machinery of their host cells to produce new viral particles
how are viruses classified into
DNA viruses
RNA viruses
Retroviruses
what are dna viruses
They contain DNA as genetic material
Viral DNA acts as a direct template for producing new viral DNA and mRNA for the synthesis of viral proteins
Examples: smallpox, adenoviruses, and bacteriophages
Bacteriophages are viruses that infect bacteria, such as the λ (lambda) phage
what are rna viruses
They contain RNA as genetic material
Most have a single strand of RNA
They do not produce DNA at all
Mutations are more likely to occur in RNA viruses than DNA viruses
Examples: tobacco mosaic virus (TMV), ebola virus
what are retroviruses
Special type of RNA virus that does produce DNA
They contain a single strand of RNA surrounded by a protein capsid and lipid envelope
Viral RNA controls the production of an enzyme called reverse transcriptase
This enzyme catalyses production of viral DNA from the single strand of RNA
The new viral DNA is incorporated into the host DNA using integrase enzymes where it acts as a template to produce viral proteins and RNA
Example: HIV (Human Immunodeficiency Virus)
what are the pathways of viral reproduction
Lysogenic
Lytic
how can a virus enter a host cell
Bacteriophages inject their genetic material into bacteria
Some animal viruses enter the cell via endocytosis by fusing their viral envelope with the host cell surface membrane
Plant viruses will often use a vector such as an insect to breach the cell wall
what is the lysogenic pathway
Some viruses will not immediately cause disease once they infect a host cell
Viral DNA known as a provirus is inserted into the host DNA, but a viral gene coding for a repressor protein prevents the viral DNA from being transcribed and translated
Every time the host DNA copies itself, the inserted viral DNA will also be copied
This is called latency and the time during which it occurs is known as a period of lysogeny
Viruses in a lysogenic state may become activated and enter the lytic pathway
Activation may occur as a result of, e.g. host cell damage or low nutrient levels inside a cell
what is the lytic pathway
The viral genetic material is transcribed and translated to produce new viral components
These components are assembled into mature viruses that accumulates inside the host cell
Eventually the host cell bursts which releases large numbers of viruses, each of which can infect a new host cell
Cell bursting is known as cell lysis
This typically results in disease
transmission of Tuberculosis
When infected people with the active form of TB cough or sneeze, the Mycobacterium tuberculosis bacteria enter the air in tiny droplets of liquid released from the lungs
TB is transmitted when uninfected people inhale these droplets
Once inside the lungs, TB bacteria are engulfed by phagocytes
The bacteria may be able to survive and reproduce while inside phagocytes
Individuals with a healthy immune system will not develop TB at this stage
This is known as the primary infection
Over time the infected phagocytes will become encased in structures called tubercles in the lungs where the bacteria will remain dormant
It is possible for the bacteria to become activated and overpower the immune system at a later stage, such as during an HIV infection when the immune system is compromised; the person will then develop TB
This is known as the active phase of TB
The length of time between infection and developing the disease can vary from a few weeks to a few years
conditions which make the population more vulnerable to TB
TB spreads more quickly among people living in overcrowded conditions
symptoms of TB
The first symptoms of TB will include developing a fever, fatigue, coughing and lung inflammation
If left untreated the bacteria will cause extensive damage to the lungs which can result in death due to respiratory failure
TB may also spread to other parts of the body where it can lead to organ failure if not treated promptly
what is and how can hiv be transmitted
HIV contains RNA and is a retrovirus
-Sexual intercourse
-Blood donation
-Sharing of needles used by intravenous drug users
-From mother to child across the placenta
-Mixing of blood between mother and child during birth
-From mother to child through breast milk
how does the replication of HIV occur
It enters the helper T cells by attaching to a receptor molecule on the host cell membrane
The capsid enters the helper T cell and releases the RNA it contains
The viral RNA is used as a template by reverse transcriptase enzymes to produce a complementary strand of DNA
Once this single-stranded DNA molecule is turned into a double-stranded molecule it can be successfully inserted into the host DNA
From here it uses the host cell’s enzymes to produce more viral components which are assembled to form new viruses
These bud from the host cell and enter the blood, where they can infect other helper T cells and repeat the process
At this stage, the individual is HIV positive and may experience flu-like symptoms
what are the different HIV infection stages
These bud from the host cell and enter the blood, where they can infect other helper T cells and repeat the process
At this stage, the individual is HIV positive and may experience flu-like symptoms
This is known as the acute HIV syndrome stage
After the initial infection period, during which HIV replication is rapid, the replication rate drops and the individual enters the asymptomatic or chronic stage
During this period the person will not show any symptoms, often for years
Gradually the virus reduces the number of helper T cells in the immune system
B cells are no longer activated
No antibodies are produced
The patient begins to suffer from HIV-related symptoms and are now in the symptomatic disease stage of the infection
The lack of T helper cells decreases the body’s ability to fight off infections, eventually leading to the final stage of an HIV infection, which is known as advanced AIDS (Acquired immune deficiency syndrome)
what happens once a patient cant produce antibodies due to hiv
As a patient can no longer produce antibodies against pathogens, they are immunocompromised and unable to fight off infections
They begin to suffer from diseases that would usually cause very minor issues in healthy individuals
These diseases are described as opportunistic
An HIV infection will progress to AIDS when
An individual starts suffering from constant opportunistic infections
The helper T cell count drops below a critical level
standard sequence of symptoms of AIDS
Initially an AIDS sufferer will only have mild infections of the mucous membranes due to the low helper T numbers
Over time, however, infections will become more severe e.g. diarrhoea, TB
During the final stages of AIDS a person will suffer from a range of more serious opportunistic infections
It is these opportunistic diseases that cause an individual with advanced AIDS to die
factors affecting how quickly HIV will progress into AIDS and how long a person with AIDS will survive
The number of existing infections
The strain of HIV the person is infected with
Their age
Access to healthcare
Routes of Entry of pathogens
Vectors
Inhalation
Ingestion
Indirect contact
Direct contact
Inoculation
how are vectors a route of entry for pathogens
These are living organisms that carry pathogens and transmit them between hosts
Insects, such as flies and mosquitoes, are common vectors for diseases
how is inhalation a route of entry for pathogens
Droplets from the respiratory tract will be suspended in the air when an infected person coughs, sneezes or talks
These droplets contain pathogens that can be inhaled by healthy people
The airways provide an entry point into the respiratory system of a new host and another infection occurs, e.g. flu, measles, tuberculosis
how is ingestion a route of entry for pathogens
Pathogens can enter through the digestive system when we ingest contaminated food or drink
This is especially probable if food is undercooked, as heat destroys most of the pathogens
These pathogens can make their way through the lining of the gut and cause disease (e.g. cholera, Salmonella poisoning)
how is indirect contact a route of entry for pathogens
Inanimate objects can contain large numbers of pathogens that may be transferred between hosts
An infected individual may touch or cough on an object which is later touched by a healthy individual who transfers the pathogens to their mouth or nose by touching their face
Examples include bedding, towels, and surfaces
how is direct contact a route of entry for pathogens
Pathogens that spread this way will require some part of the host, e.g. skin, body fluids, to come into direct contact with a healthy individual
Pathogens that spread by this route can then pass through the mucous membranes and enter the bloodstream, e.g.
When shaking hands with another person who then puts their hand to their nose or mouth
During sexual transmission
Examples include HIV, ebola, syphilis
how is inoculation a route of entry for pathogens
This typically occurs when a pathogen enters the body through broken skin, providing it with a direct route into the bloodstream
Transmission could be through sexual contact, sharing needles during drug use, or bites or scratches from infected animals
Examples include hepatitis B, HIV, tetanus, and rabies
what are the barriers to Pathogenic Entry
Skin
Microorganisms of the gut and skin
Stomach acid
Lysozyme
how does the skin act as a barrier to pathogenic entry
The skin provides a physical barrier against infection
If the skin is damaged it leaves the exposed tissue beneath vulnerable to pathogens
The blood clotting mechanism of the body plays an important role in preventing pathogen entry in the case of damage to the skin
Blood clotting takes time, however, so a few pathogens may still enter before a clot forms
how does microorganisms of the gut and skin act as a barrier to pathogenic entry
Collectively these harmless microorganisms are known as the gut or skin flora
They compete with pathogens for resources, thereby limiting their numbers and therefore their ability to infect the body
how does the stomach acid act as a barrier to pathogenic entry
The hydrochloric acid that makes up a large part of the gastric juices in the stomach creates an acidic environment that is unfavourable to many pathogens present on food and drink
Sometimes a few of these pathogens may survive and make their way to the intestines where they infect the gut wall cells and cause disease
how does lysozymes act as a barrier to pathogenic entry
Secretions of the mucosal surfaces, e.g. tears, saliva, and mucus, contains an enzyme called lysozyme
This enzyme will damage bacterial cell walls, causing them to burst, or lyse
what are the types of immune response in the body once a pathogen enters
Non-specific
Specific
what does a non-specific immune response mean
This response is the same, regardless of the pathogen that invades the body
what does a specific immune response mean
This is a response specific to a particular pathogen
The immune system is able to recognise specific pathogens due to the presence of antigens on their cell surface
Pathogens have non-self antigens, so the immune system recognises them as not belonging to the body
what does the non-specific immune response mean
Inflammation
Interferons
Phagocytosis
why does inflammation occur
Body cells called mast cells respond to tissue damage by secreting the molecule histamine
Histamine is a chemical signalling molecule that enables cell signalling, or communication between cells
what does histamine stimulate
Vasodilation increases blood flow through capillaries
Capillary walls become ‘leaky’, or more permeable, allowing fluid to enter the tissues and creating swelling
Some plasma proteins leave the blood when the capillaries become more permeable
Phagocytes leave the blood and enter the tissue to engulf foreign particles
Cells release cytokines, another cell signalling molecule that triggers an immune response in the infected area
why do interferons help in the non-specific immune response
Cells infected by viruses produce anti-viral proteins called interferons
Interferons prevent viruses from spreading to uninfected cells
They inhibit the production of viral proteins, preventing the virus from replicating
They activate white blood cells involved with the specific immune response to destroy infected cells
They increase the non-specific immune response e.g. by promoting inflammation
mode of action of phagocytosis
Chemicals released by pathogens, as well as chemicals released by the body cells under attack, e.g. histamine, attract phagocytes to the site where the pathogens are located
They move towards pathogens and recognise the antigens on the surface of the pathogen as being non-self
The cell surface membrane of a phagocyte extends out and around the pathogen, engulfing it and trapping the pathogen within a phagocytic vacuole
This part of the process is known as endocytosis
Enzymes are released into the phagocytic vacuole when lysosomes fuse with it
These digestive enzymes, which includes lysozyme, digest the pathogen
After digesting the pathogen, the phagocyte will present the antigens of the pathogen on its cell surface membrane
The phagocyte becomes what is known as an antigen presenting cell
The presentation of antigens initiates the specific immune response
what is the function of the antibody
Antibodies bind to specific antigens that trigger the specific immune response
Pathogens enter host cells by binding to them using receptors on their surface; antibodies can bind to these receptors, preventing pathogens from infecting host cells
Antibodies can act as anti-toxins by binding to toxins produced by pathogens, e.g. the bacteria that cause diphtheria and tetanus; this neutralises the toxins
Antibodies cause pathogens to clump together, a process known as agglutination; this reduces the chance that the pathogens will spread through the body and makes it possible for phagocytes to engulf a number of pathogens at one time
types of lymphocytes
T cells
B cells
where are T-cells made
T cells are produced in the bone marrow and finish maturing in the thymus
Mature T cells have specific cell surface receptors called T cell receptors
These receptors have a similar structure to antibodies and are each specific to a particular type of antigen
how can T cells be activated
T cells are activated when they encounter and bind to their specific antigen on the surface of an antigen presenting cell
These activated T cells divide by mitosis to increase in number
Dividing by mitosis produces genetically identical cells, or clones, so all of the daughter cells will have the same type of T cell receptor on their surface
types of t cells
T helper cells
T killer cells
T memory cells
how do t helper cells contribute to the specific immune response
Release chemical signalling molecules that help to activate B cells
Release chemical signalling molecules that help to activate T killer cells
Release chemicals called opsonins that label pathogens and infected cells for phagocytosis
how do t killer cells contribute to the specific immune response
Bind to and destroy infected cells displaying the relevant specific antigen
how do t memory cells contribute to the specific immune response
Remain in the blood and enable a faster specific immune response if the same pathogen is encountered again in the future
how is B cells job in the immune system
If the corresponding antigen enters the body, B cells with the correct cell surface antibodies will be able to recognise it and bind to it
When the B cell binds to an antigen it forms an antigen-antibody complex
The binding of the B cell to its specific antigen, along with the cell signalling molecules produced by T helper cells, activates the B cell
Once activated the B cells divide repeatedly by mitosis, producing many clones of the original activated B cell
types of B cells
Effector cells, which differentiate into plasma cells
-Plasma cells produce specific antibodies to combat non-self antigens
Memory cells
-Remain in the blood to allow a faster immune response to the same pathogen in the future
types of immunity
Active immunity
Passive immunity
types of active immunity
Natural; acquired through exposure to pathogens
Artificial; acquired through vaccination
types of passive immunity
Natural-Foetuses receive antibodies across the placenta from their mothers
-Babies receive antibodies in breast milk
Artificial-People can be given an injection / transfusion of antibodies e.g. the tetanus antitoxin
The antibodies will have been collected from people or animals whose immune system had been triggered by a vaccination to produce antibodies
As the person’s immune system has not been activated, there are no memory cells that can enable antibody production in a secondary response; if a person is reinfected they would need another infusion of antibodies
events developing immunity
The immune system is activated when a new antigen is encountered, launching a primary immune response consisting of a non-specific immune response followed by a specific immune response
the numbers of T and B cells with the correct membrane receptors present in the blood will be low
It will take time for the correct T and B cells to be activated and to divide and differentiate into different cell types
It can take several days before plasma cells develop and are able to start producing antibodies against an antigen
This is the reason why an infected person will experience symptoms of the disease the first time they contract it
Both T and B cells produce memory cells during the primary response, which will remain in the blood after an infection is over
The presence of memory cells means that a person is said to be immune to the pathogen
Should the immune system encounter the same antigen again in the future it will launch a secondary immune response which will be much faster and stronger than the primary response
what occurs in a secondary immune response
Memory cells are present in larger quantities than the mature lymphocytes at the start of the primary response, so the correct memory cells are able to detect an antigen, activate, divide by mitosis, and differentiate much more quickly
Antibodies are produced more quickly and in larger quantities in a secondary response
This will often eliminate the pathogen before the infected person can show symptoms
what are HIV evasion mechanisms to win the evolutionary race
HIV shows antigenic variability due to the high mutation rate in the genes coding for antigen proteins
The virus prevents infected cells from presenting their antigens on the cell surface membrane, making it very difficult for the relevant white blood cells to recognise and destroy the infected cells
what are TB evasion mechanisms to win the evolutionary race
Once engulfed by phagocytes in the lungs the bacteria produce substances that will prevent a lysosome from fusing with the phagocytic vacuole
This prevents the bacteria from being broken down by digestive enzymes, leaving them to multiply within the phagocyte
As with HIV the bacteria can disrupt antigen presentation in infected phagocytes, making it difficult for the immune system to recognise and destroy these cells
types of antibiotics
Bactericidal; they kill bacterial cells
Bacteriostatic; they inhibit bacterial growth processes
hospital measures to prevent the spread of HAIs
Staff and visitors must wash hands regularly while visiting patients
If a person contracts a HAI they should be moved to an isolation ward to prevent spread of the infection
Surfaces and equipment must be disinfected after every use
hospital practices developed to reduce the risk of antibiotic resistant HAIs
No antibiotic prescriptions for minor infections or viral diseases
No use of antibiotics as a preventative measure against infections
Prescription of a narrow-spectrum antibiotic to treat the infection
-Narrow-spectrum antibiotics are active against a narrow range of bacterial infections, as opposed to broad-spectrum antibiotics which are effective against many types of bacteria
The advantage of using narrow-spectrum antibiotics is that any resistance genes that arise will not cause problems if they are transferred to other types of bacteria
Rotate the use of different antibiotics to decrease the chance of bacteria developing resistance against one antibiotic
how do decomposers break down matter and therefore contribute to the gas concentrations in the air
These decomposers secrete enzymes that break large organic molecules, such as cellulose, down into smaller ones
These small molecules, such as glucose, can be broken down further during respiration
During decomposition they also release waste products which provides nutrients to plants
The microorganisms involved in decomposition produce CO2 and methane which are released into the atmosphere
Carbon dioxide can then be absorbed by green plants which will fix the carbon back into carbohydrates during photosynthesis
how is having a unique DNA profile studied by PCR useful?
forensic science as it provides a way to identify individuals
DNA profiling can also be used to determine the genetic relationships between different organisms e.g.
Paternity and maternity testing
Ancestry kits
Determining evolutionary relationships between different species
how can DNA profiles be created
Isolating a sample of DNA e.g. from saliva, skin, hair, or blood
Producing more copies of the DNA fragments in the sample using the polymerase chain reaction (PCR)
Carrying out gel electrophoresis on the DNA produced by PCR
Analysing the resulting pattern of DNA fragments
what does Each PCR reaction require
DNA or RNA to be amplified
Primers( short sequences of single-stranded DNA that have base sequences complementary to the 3’ end of the DNA or RNA being copied; they define the region that is to be amplified, identifying where the DNA polymerase enzyme needs to bind)
DNA polymerase
The enzyme used to build the new DNA or RNA strand.
Taq polymerase does not denature at the high temperature required during the first stage of the PCR reaction
Free nucleotides (Enable the construction of new DNA or RNA strands)
Buffer solution (Ensures the optimum pH for the reactions to occur in)
three main stages of the PCR reaction
Denaturation
Annealing
Elongation / Extension
what does the denaturation stage in the PCR reaction consist
The double-stranded DNA is heated to 95 °C which breaks the hydrogen bonds that hold the two DNA strands together
what does the annealing stage in the PCR reaction consist
The temperature is decreased to 50-60 °C so that primers can anneal to the ends of the single strands of DNA
what does the elongation stage in the PCR reaction consist
The temperature is increased to 72 °C, as this is the optimum temperature for Taq polymerase to build the complementary strands of DNA to produce the new identical double-stranded DNA molecules
when enough PCR cycles have occured, what are the next steps?
After PCR is completed the DNA is treated with restriction endonuclease enzymes and a fluorescent tag can be added; both in preparation for gel electrophoresis
Restriction endonucleases break the DNA up into fragments of different length
Fluorescent tags enable the DNA fragments to be seen under UV light
what does gel electrophoresis consist of?
DNA fragments are created, e.g. using enzymes known as restriction endonucleases that cut DNA at specific restriction sites
The resulting fragments are inserted into a well at the end of a piece of agar gel, before a current is passed through the gel
why is a potential difference used in gel electrophoresis
Positively charged molecules will move towards the cathode (negative pole) while negatively charged molecules will move towards the anode (positive pole)
DNA is negatively charged due to the phosphate groups and so when placed in an electric field the molecules move towards the anode
what affects the rate at which dna fragments travel in gel electrophoresis
The molecules are separated according to their size / mass
Different sized molecules move through the gel at different rates
The tiny pores in the gel allow smaller molecules to move quickly, whereas larger molecules move more slowly
stages of gel electrophoresis
An agarose gel plate is created and wells are cut into the gel at one end
The gel is submerged in a tank containing electrolyte solution which conducts electricity
The DNA samples are transferred into the wells using a micropipette, ensuring that a sample of DNA standard is loaded into the first well (control group)
The negative electrode is connected to the end of the plate with the wells and the positive anode is connected at the far end
The DNA fragments move towards the anode due to the attraction between the negatively charged phosphates of DNA and the anode
The smaller mass / shorter pieces of DNA fragments move faster and therefore further from the wells than the larger fragments
Probes are then added, after which an X-ray image is taken or UV-light is shone onto the paper producing a pattern of bands which can be compared to the control, or standard, fragments of DNA
what are probes
Probes are single-stranded DNA sequences that are complementary to the regions of interest; they can be
A radioactive label which causes the probes to emit radiation that makes the X-ray film go dark, creating a pattern of dark bands
A fluorescent dye which fluoresces when exposed to UV light, creating a pattern of coloured bands
how are the bands in gel electrophoresis created
The fragments were produced after PCR by cutting the DNA samples into pieces using restriction endonuclease enzymes
Restriction endonucleases cut DNA at specific locations in the DNA base sequence, so will always cut in between sections of repeated bases known as variable number tandem repeats (VNTRs)
VNTRs are known as micro- or mini-satellites depending on the number of repeats that occur
Different people have different numbers of repeats in their VNTR regions, so the fragments will differ in length depending on whether there are few or many repeats
how is gel electrophoresis used to identify individuals
Different individuals will have different lengths of DNA fragments, so a different pattern of banding will form on each profile
Every banding pattern will be unique to an individual, so comparisons of DNA from crime scenes with that of suspects is a reliable way of finding out who was present at a crime scene
how can DNA profiling be useful in selective or captive breeding programmes of animals or cultivation of plants
DNA profiles of the particular organisms can be compared to determine which are genetically the most different from each other
These organisms will then be crossbred, ensuring that the individuals that breed together are not closely related
why do we breed species together that are not closely related
inbreeding, and can cause genetic problems at an individual and population level such as:
In individuals there can be an accumulation of harmful recessive alleles that might otherwise have been masked by healthy dominant alleles
Inbreeding leads to a smaller gene pool within a population, which can reduce a population’s ability to adapt to change
factors to accurately estimate TOD (time of death)
Extent of decomposition
Stage of succession
Forensic entomology
Body temperature of the deceased
The degree of muscle contraction
what happens in the first stage of decomposition
Decomposers break down cells and tissues over the course of a few days
At this stage in decomposition the appearance of the skin can be a helpful indication of time since death; skin will often appear greenish in colour
what happens in the second stage of decomposition
breakdown of tissues and organs by micro-organisms over the course of a few days or weeks
This process produces gases, such as methane, which will lead to bloating
The skin will blister and fall off the rest of the body
what happens in the last stage of decomposition
A few weeks after death the remains of the soft tissues will turn to liquid which becomes visible as it leaves the body
This process will continue over the course of months or years until only a skeleton remain
After a few decades or centuries, the skeleton will disintegrate until nothing remains
what factors affect decomposition
temperature and availability of oxygen
Decomposition would be slower in anaerobic conditions and at lower temperatures but would be faster at high temperatures
how is succession different in ecology than in forensics
in an ecosystem the early pioneer species are out-competed and disappear as the system matures, while in a dead body all of the newly arriving species remain as decomposition progresses
stages of succession of a body above the ground
Bacteria will be found in and on the dead body immediately after TOD
As tissue decomposition sets in it creates ideal conditions for flies to lay eggs and their larvae to hatch
As more soft tissue is consumed by the fly larvae it creates favourable conditions for beetles to establish
When tissue dries out over time flies will leave the body as they prefer a moisture-rich environment
Beetles, however, can decompose dry tissue so they will remain on the body
Once all tissues have been decomposed most organisms will leave the body
what factors affect the insects found in a body while decomposing
accessibility to insects and availability of oxygen will be affected e.g.
Buried in soil
Buried in a coffin
Under water
Factors that affect the progression of insect life cycles
Drugs that may be present in the body
Humidity of the surroundings
Oxygen availability
Temperature
what is algor mortis
Once a person dies metabolic reactions will eventually come to an end
Since no more heat is produced the body temperature drops until it reaches the temperature of the surrounding environment
conditions which affect the rate at which body heat is lost
Air temperature
Surface area : volume ratio
Presence of clothing
Percentage body fat
what is rigor mortis
Muscles in the body begin to contract about 4-6 hours after TOD, leading to a general stiffening of the body
why does rigor mortis occur
changes to the proteins in muscle cells after death
Since no more oxygen reaches the muscle cells after death they will start to respire anaerobically, producing lactic acid
The accumulation of lactic acid decreases the pH in the muscle cells, denaturing the enzymes that produce ATP
Without ATP the myosin heads cannot be released from the actin filaments, locking the muscles in a contracted state
Muscles contract due to the action of two protein filaments; myosin and actin
The binding of myosin heads to actin proteins followed by the bending of the myosin heads causes muscle contraction
ATP is required to allow the myosin heads to detach from the binding sites on actin
how can rigor mortis help estimate TOD
Rigor mortis will begin in the smaller muscles of the head and end in the larger muscles of the lower body
what is the process of rigor mortis affected by
level of muscle development and the temperature of the surroundings
Higher temperatures will speed up the rate of rigor mortis
