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    I'm posting up my notes for unit 5. They cover the main bits of what we need to know from what the NAS book says. Some of it might not be very good (alot of this chapter is dull) but here we go:

    Photosynthesis


    Chloroplasts
    Chloroplasts have internal membranes called thylakoids – situated in the stroma. Thylakoids arranged in stacks are called grana.

    Light --> chemical energy conversion happens in the thylakoids and the Calvin cycle happens in the stroma.

    Photosynthetic organisms contain light absorbing pigments, mainly chlorophylls and carotenoids.
    Chlorophyll exists as type a (most abundant) and b. They absorb red and blue-violet light, reflecting green.
    Carotenoids absorb blue-violet light and appear a yellowy-orange colour. An example is β-carotene.

    Absorption and action spectra
    A graph of relative absorbance of different wavelengths of light by a pigment is known as an absorption spectrum.
    The amount of photosynthesis at different wavelengths is know as an action spectrum. The two tend to resemble one another, showing that the pigments are involved in photosynthesis.

    The Light-dependent reaction (LD)
    This occurs in the thylakoids.
    The photosynthetic pigment molecules are arranged into photosystem I (PSI) or photosystem II (PSII) and two different types exist – primary and accessory. Two different forms of chlorophyll a are primary pigments. One has an absorption peak at 680nm and is found in PSII and the other has an absorption peak at 700nm and is found in PSI.
    All other forms of chlorophyll and the carotenoids are accessory pigments which pass on their energy to primary pigments.

    Electrons in chlorophyll molecules in PSI and PSII become excited by light energy and become high-energy electrons. They are emitted when light is absorbed and are taken up by electron acceptors, which pass them on along a chain of electron carriers in a series of redox reactions. Because each carrier is at a lower energy level than the last, enough energy is released to form ATP from ADP and Pi. Some energy is used to move H+ ions across from the stroma. These diffuse back in (down the concentration gradient) through proteins with ATP synthetase and ATP is formed.

    Electrons lost are replaced by the photolysis of water, catalysed by an enzyme associated with PSII:
    H2O --> 2H+ + ½ O2 + 2e-
    Oxygen is released as a waste product of photosynthesis.

    Non-cyclic photophosphorylation involves electrons from PSI passing to an electron carrier (NADP), which then combines with H+ ions to form NADPH. This process doesn’t result in any ATP formation.

    Cyclic photophosphorylation only involves PSI. The excited electron from PSI is passed to electron carriers used in PSII and then return to PSI again. ATP is still made in this process but no NADPH is made and no oxygen is evolved.

    Light Independent reaction (LI)
    This occurs in the stroma and requires ATP for energy and NADPH (from the LD reaction) to reduce molecules. In this reaction, CO2 is reduced to carbohydrate.

    The Calvin cycle:
    A molecule of CO2 combines with a 5C pentose – RuBP, forming 2 molecules of glycerate 3-phosphate. This process is called carboxylation and is catalysed by RuBisCO. ATP phosphorylates the glycerate 3-phosphate and then it is reduced by NADPH. It can then be used to either:
    · Regenerate RuBP so the cycle can continue (5 molecules are needed)
    · Build up organic compounds e.g. starch. (1 molecule is left for this)

    Environmental factors that affect photosynthesis
    The limiting factor is a single factor that limits photosynthesis of the plant. For example if light intensity is low it is the limiting factor. If it is increased the rate of photosynthesis increases until another factor becomes limiting.

    The concentration of carbon dioxide also affects the rate of photosynthesis. The higher the concentration the faster the rate of photosynthesis.

    Temperature affects the rate of chemical reactions and is important in the LI stage as it is enzyme controlled (RuBisCO).

    Mineral Nutrition

    Nitrogen and Sulphur needed for amino acid synthesis.
    Phosphorus for nucleic acid and phospholipid synthesis.
    Potassium for cell sap.
    The elements are taken up as inorganic ions through root hairs. Their uptake is active so requires energy.

    Growth control in plants

    Detection of light in plants
    Germination is affected by red & far-red light. R promotes and FR inhibits. Light is detected by photoreceptors (called phytochrome).
    Phytochrome exists as PR (absorbs red light) and PFR (absorbs far-red light).
    When PR absorbs red light it is converted to PFR and PFR is converted to PR when it absorbs far-red light. So in the daylight theres a lot of Pr present as there is a lot of red light. PFR is slowly converted back to PR in the dark.

    Phototropism
    Tropisms are growth responses to gravity and light. Growth towards a stimulus is positive (e.g. shoots are positively phototropic) and away from a stimulus is negative (e.g. shoots are negatively geotrophic).

    Plant growth substances
    Growth promoters – auxins, gibberellins, cytokinins
    Growth inhibitors (or antagonists to growth promoters) – ABA, ethene.

    They can interact synergistically (together they enhance effects) or antagonistically (the effects counteract each other).

    Auxins promote cell division by increasing the plasticity of cell walls making them less turgid. Water moves into the cells and they grow in size. Auxins also encourage fruit development, lateral root development and apical dominance. They delay abscission.
    Synthetic auxins may be used to encourage rooting in cuttings or used as selective herbicides (because high concentrations disrupt broad leaved plants).

    Gibberellins encourage bolting in long-day plants in short-day conditions, fruit development, germination, stem elongation and the release of alpha amylase from seed embryos.

    Cytokinins delay senescence and encourage the maturation of chloroplasts, lateral bud development and root & shoot development.

    ABA (abscisic acid) encourages dormancy, senescence and stomatal closure as well as inhibiting growth.

    Ethene promotes abscission and ripening of fruits.

    Classification

    The 5 Kingdom system recognises these 5 groups:
    · Prokaryotae – prokaryotes (lack membrane bound organelles and a true nucleus).
    · Protoctista – eukaryotes which are not fungi, plants or animals.
    · Fungi – non photosynthetic eukaryotes usually with spores and hyphae.
    · Plantae – multicellular, photosynthetic eukaryotes with cellulose cell walls.
    · Animalia – multicellular, non photosynthetic eukaryotes with nervous coordination.

    Taxonomy groups species as follows:
    · Kingdom
    · Phylum
    · Class
    · Order
    · Family
    · Genus
    · Species

    Distribution

    Distribution of organisms is affected by:
    Abiotic = physical factors
    Biotic = effects of other living organisms.

    Abiotic factors may include temperature, light, wind, water availability, soil condition, altitude, aspect and steepness.

    Succession

    Succession is the progressive change occurring in a community of organisms over a period of time. It takes place in a number of stages and results in long-term changes.

    An area may first be colonised by an organism such as algae – the pioneer community. Organic material accumulates to form soil which supports other organisms. Larger plants replace smaller ones until woodland/forest (the climax community) forms. The succession from bare rock --> forest is called a sere.
    Bare rock --> forest is primary succession. Succession on land which had vegetation on it before is called secondary succession.

    A balance is eventually reached between plants and the environment – the climatic climax. Human interference can prevent succession from reaching its natural climax and leads to a deflected succession.

    Populations

    A population is a group of individuals of one species occupying the same area.
    A community is all living organisms in a habitat.

    The maximum population size that can be sustained by a particular habitat is called its carrying capacity. Disease, competition and predation are factors which limit population growth (environmental resistance).

    Population size is affected by density-dependent & density-independent factors.
    Density-dependent = any factor limiting population size whose effect is proportional to the population density (mainly biotic).
    Density-independent = any factor limiting population size whose effect is independent of the population density (mainly abiotic).

    Competition for resources may be intraspecific or interspecific competition.
    Intraspecific competition occurs between members of the same species whereas interspecific competition occurs between different species (usually of the same trophic level).

    Controlling insect populations

    Population can be controlled chemically using insecticides (natural or artificial). The problems with using insecticides include the death of harmless organisms, may not be biodegradable, pests may develop resistance to it and it might bioaccumulate in food chains.

    The other option is a biological control – using a predator or parasite to control the pest population.
    It is useful because it is specific, does not damage the environment, requires fewer applications and there is less of a problem with pests becoming resistant.
    However, the result is often slower than chemicals, the predators may not stay in the area, or may become pests themselves.

    Some farmers may encourage natural predators, for example, by intercropping.

    The best way to control pest populations is by using a variety of methods.

    Conservation

    Conservation is maintaining ecosystems to achieve maximum biodiversity. Coppicing is a good way of achieving this, whilst still providing resources.

    Managing grassland

    Mowing
    - Is unselective.
    - Cut vegetation may be removed for use as hay but this removes nutrients from the area.
    - Mowings left on the ground may smother some plants.

    Grazing
    - Animals are selective in what they eat.
    - Dung provides nutrients.
    - Trampling sometimes becomes an issue.

    Wet grasslands
    - In summer, meadows provide hay and an area for grazing.
    - Often flooded in winter, attracting birds.
    - Prolonged flooding may be harmful to some vegetation.

    Scrub clearance
    - Regular cutting back of scrub creates a habitat similar to coppice.

    Using fire
    - Controls shrubby growth where machine use is difficult.
    - Danger to animals who cannot escape.

    The EU Habitats Directive’s priorities are to create a European ecological network of special areas of conservation and to encourage conservation in agriculture, regional development and transport.

    Genes, alleles and variation

    A gene is a length of DNA that codes for a particular protein to be produced.
    An allele is a different form of a particular gene.

    Discontinuous variation has clear-cut differences. E.g. eye colour.
    Continuous variation has no separate categories.

    Monohybrid inheritance – inheritance of a single characteristic.
    Genes are found on specific sites on the chromosome called the locus.

    Genotype is the genetic composition of an organism and the phenotype is the appearance of the genotype.

    Monohybrid cross
    Involves a single character that is controlled by one gene with 2 or more alleles.

    Sometimes a heterozygous genotype may contain no dominant alleles (incomplete dominance) so both alleles equally contribute to the phenotype e.g. red & white flowers crossed may produce some pink ones.

    In codominance, 2 alleles are both expressed in the phenotype of a heterozygous organism such as in sickle cell anaemia.

    3 or more alleles for a specific locus means that the gene has multiple alleles. This is shown in blood groups where IA, IB and IO are involved. IA & IB are codominant but IO is recessive. The multiple allele system can also be seen in rabbit coat colours.

    Dihybrid inheritance is the inheritance of 2 different characteristics, controlled by genes at different loci (if genes are on the same loci, linkage will show).

    Recombination is when new combinations of characters arise and this can lead to variation.

    Linkage describes the relationship between different genes located on the same chromosome. Genes on a particular chromosome will normally be inherited together, unless they are separated during crossing-over.
    Complete linkage (no crossing-over occurs during meiosis) is rare.
    A ratio of 9:3:3:1 is only the expected ratio. It is often different due to linkage. You can check for linkage by doing a test cross.

    One gene may interfere with the expression of another. This is known as epistasis.

    Genetic variation

    Meiosis leads to genetic variation because recombination can result during crossing-over in prophase I and there is a random assortment of chromosomes in metaphase I. There is also random fertilisation during sexual reproduction.

    A mutation is a change in the DNA code and leads to further variation.
    Mutagens increase the rate of mutation. Most are harmful, some are beneficial.

    The type of mutation that might occur:
    - point (gene) mutation – a change in the base sequence by the deletion, insertion or substitution of a base, resulting in a different protein being produced. Sickle cell anaemia arose due a point mutation.
    - Chromosome mutations – a change in the structure or number of chromosomes. Structure can be altered by deletion (breaking of the chromosome during division) or translocation (part of one chromosome attaches to another – Down’s symdrome can be caused by this).
    Numerical changes may involve the duplication/loss of one chromosome (polysomy) or the duplication of every chromosome, giving 3 complete sets (polyploidy).

    Polysomy – where a particular chromosome isn’t diploid. It is usually caused by non-disjunction (failure of homologous chromosomes to separate) during meiosis, leaving one daughter cell with 2 chromosomes rather than 1.

    Polyploidy – organisms with 3 or more sets of chromosomes. Chromosomes fail to separate during cell division. In autopolyploidy, all chromosomes come from the same species but in allopolyploidy, chromosomes come from 2 different species.
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    Wow! I'd rep you again if I could =)
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    Environmental change and evolution

    3 types of natural selection:
    - Directional selection – favours one extreme of variation.
    - Disruptive selection – favours both extremes of variation, eliminating those in middle range.
    - Stabilising selection – favours the mean of the distribution.

    Isolation & speciation
    Geographical isolation may result in allopatric speciation. Speciation may also arise as a result of behavioural isolation. This may result in sympatric speciation.

    Gene technology

    Gene technology changes characteristics of an organism by inserting genes from another – this gives recombinant DNA.

    Restriction endonucleases cut at sites within a DNA strand at specific places called recognition sites. They leave a staggered cut with complementary ends known as ‘sticky ends’.

    Plasmids are small loops of DNA found in bacterial cells. They can be used to introduce a particular gene into a host cell.
    Restriction endonucleases cut open the plasmid and the gene – leaving complementary sticky ends.
    DNA ligase will join the gene and plasmid together.
    The altered plasmid is then inserted into a bacterial cell which will grow and excrete the product.

    Reverse transcriptase forms DNA from an RNA template. Gene technology is useful because insulin and other human proteins can be produced on a large scale.

    Chymosin production
    Chymosin coagulates proteins in milk.
    It used to be taken from calf stomachs.
    The same DNA code from calves is incorporated into a yeast cell so the same product is made.

    The polymerase chain reaction
    Used to replicate a particular sequence of DNA. It can increase the quantity of genetic material and only takes a short time.
    - the sample of DNA is heated to 95oC so that the H bonds between the strands break, leaving 2 separate strands.
    - At 40oC, DNA polymerase builds a complementary strand to each, reforming double stranded DNA.
    - These steps are repeated.

    PCR is useful in genetic fingerprinting:
    - DNA is isolated from blood
    - Restriction endonucleases cut the DNA into a number of different-sized fragments.
    - Electrophoresis separates the pieces, so they show up in bands. The positions of these bands can then be compared to other samples.
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    (Original post by Ellie4)
    Wow! I'd rep you again if I could =)
    Well I thought I may as well post it since I've been doing this for 3 days (I'm sloooowww)
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    Hehe coolies I don't think i've given out my rep today - i'll check and give you some if i can!!
    Have you seen my ones for synoptic?
    http://afterhours.hopto.org/phpBB2/index.php
    If you haven't seen them already
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    (Original post by Bekaboo)
    Hehe coolies I don't think i've given out my rep today - i'll check and give you some if i can!!
    Have you seen my ones for synoptic?
    http://afterhours.hopto.org/phpBB2/index.php
    If you haven't seen them already
    Yep they are really helpful!! Thankies
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    thanks alot!!!!!!!!!!!!!!!!!!!! omg... i was soo worried about unit 5 and here u r providing us with great notes thanks alot!!! do u have any notes for option a?! especially the second chapter (the culture medias) plz plz!! thanks!
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    'increasing the plasticity of cell walls'

    what is plasticity?
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    (Original post by Revenged)
    'increasing the plasticity of cell walls'

    what is plasticity?
    The book says plasticity. I think its softening of the cell wall but the book isn't too clear. Maybe elasticity would be a better word.
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    (Original post by Revenged)
    'increasing the plasticity of cell walls'

    what is plasticity?
    Yeah, the walls become less rigid, so the cell becomes larger and it no longer turgid, so that it can take up more water.
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    cheers!
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    (Original post by ossoss87)
    thanks alot!!!!!!!!!!!!!!!!!!!! omg... i was soo worried about unit 5 and here u r providing us with great notes thanks alot!!! do u have any notes for option a?! especially the second chapter (the culture medias) plz plz!! thanks!
    Option A is micro isn't it?? Gimme a sec while i trawl my computer. I took it in January so i'm not making new notes cos it won't be on synoptic... but i might have some notes on here. And there shud b a quiz on that site for micro

    Ok no notes on this computer... may be some downstairs
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    yes its option a! plz try ur best for finding them plz.. i neeed them soo badly plz!!! plz... thanks alot!

    (Original post by Bekaboo)
    Option A is micro isn't it?? Gimme a sec while i trawl my computer. I took it in January so i'm not making new notes cos it won't be on synoptic... but i might have some notes on here. And there shud b a quiz on that site for micro

    Ok no notes on this computer... may be some downstairs
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    btw what did u get in the exam?
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    Damn!! this paper seems so much easier than most previous papers!!Even the mark scheme seemed ok...This probably means our paper next week is gonna be a beast..just great...sods bluddy law..
    Gd luk all
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    (This paper = Jan 05 paper btw)
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    has anyone got any notes for gene technology - genetic finger prints etc they wouldnt mind posting?!?!
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    Okay, erm, this isn't Edexcel, it's stuff from my board so i dunno what bits you need to know but I'll post it anyway...

    Genetic Fingerprinting - Method

    - DNA extracted from cell sample
    - cut by restriction enzyme
    - enzymes cut close to, but not within VNTRs
    - fragments can be separated according to size
    - by agarose gel electrophoresis
    - fragments placed in well at one end of gel
    - PD applied
    - fragments move towards anode
    - smaller fragments move further
    - bands of DNA can be revealed by fluorescent stain
    - DNA fragments transferred to nylon membrane by Southern blotting
    - DNA fragments denatured by heating to give single stranded DNA
    - radioactive probe has complementary base sequence to VNTR
    - probe binds with complementary single stranded DNA
    - x-ray film used to locate radioactive probe
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    thanks!!
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    More genetic fingerprinting stuff:

    - VNTRs found in DNA which does not code for a gene
    - no. of repeats varies markedly between individuals
    - is inherited
    - half of repeats from each parent
    - only identical twins have same genetic fingerprint
 
 
 
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