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SNAB AS Biology Unit 2 Topic 4 Revision notes

These notes do not cover absolutely everything, but they do cover those major topics and the wording you seem to have the greatest difficulty with. The numbered points come directly from the SNAB syllabus. 1) Compare the ultrastructure of plant cells (cell wall, chloroplasts, amyloplasts, vacuole, tonoplast, plasmodesmata, pits and middle lamella) with that of animal cells.

Cell wall layer of tough cellulose fibrils which surrounds all plant cells provides mechanical strength, rigidity and support for the cell prevents the cell from bursting Chloroplasts lens shaped many internal membranes (called lamellae) which contain chlorophyll (each lamella is called a thylakoid, and a stack of thylakoids forms a granum) the sites of photosynthesis which traps light energy and uses it to produce carbohydrates (sugar etc) from carbon dioxide and water. Vacuole large central organelle in most plant cells, usually nearly fills the cell surrounded by a membrane called the tonoplast full of fluid (= cell sap; solution of sugars, mineral salts etc) used for storage e.g. sucrose; produce turgor pressure (essential for support) Amyloplasts A type of membrane-bound organelle called a plastid containing starch (often called starch grains) Plamosdesmata Minute pores through the cell wall with cytoplasmic connections continuous with the cytoplasm in adjacent cells Middle lamella Layer between cell walls of adjacent plant cells Joins the cells together Made of a glue-like material containing polysaccharides called pectins

2) Compare the structure and function of the polysaccharides starch

and cellulose including the role of hydrogen bonds between glucose molecules in the formation of cellulose microfibrils. Cellulose: -glucose molecules joined by 1,4 glycosidic bonds alternate -glucose molecules are rotated through 180o the chains can be very long with between 1000 10 000 glucose molecules this results in the cellulose molecule forming a very long straight unbranched chain the hydroxyl (-OH) groups project from both sides of the chain the strength of the cell wall comes from cellulose microfibrils (bundles of 60 70 straight unbranched cellulose molecules can lie parallel and held together by hydrogen bonds to form cellulose microfibrils) spaces between the microfibrils make cell wall freely permeable and can also hold water and allow water to travel by microcapillary action Starch Polymer of -glucose Composed of two aglucose polymers Unbranched amylose and branched amylopectin Starch molecules form a helix Compact 3D structure with lots of ends Acts as a store of glucose molecules from which glucose can be released when required Cellulose Polymer of -glucose Only one polymer Long straight unbranched chains Cellulose molecules are straight Cellulose chains held together by hydrogen bonds to form bundles Acts as a strong flexible structural component of cell walls

3) Explain how the arrangement of cellulose microfibrils in plant cell


walls and secondary thickening contribute to the physical properties of plant fibres, which can be exploited by humans. Location of cells for mechanical support Sclerenchyma and xylem are located in the vascular bundles around the outside edge of the stem This provides maximum resistance to compression forces (from weight of shoot system) and bending forces imposed by the wind How are tall trees supported? As plants get taller they need more strengthening to withstand compression from the increasing mass of the shoot bending forces from the effect of wind on the larger plant body

This is achieved by division of the cambium (in vascular bundles, between xylem and phloem) which produce more xylem, making wood, which produces the characteristic annual rings; one ring per year. The distinction between one ring and the next is due to the differing sizes of the xylem vessels produced: in spring the vessels are large but in summer they are smaller Xylem cells are produced by differentiation of the unspecialised cells produced by the cambium - xylem cell genes are switched on to produce the characteristics of a xylem vessel Water transport through xylem vessels Learn this wording: Water constantly evaporates from the surface of the cells in the substomatal cavity The water lost is replaced by water moving across the leaf by capillary action through the cell walls This, in turn, draws water out of the xylem vessels Hydrogen bonding between water molecules, called cohesion, allows continuous columns of water molecules to be pulled up the xylem by the transpiration stream to replace the water lost by the leaf. Hydrogen bonding between the water molecules and the cellulose and lignin of the xylem vessel walls, called adhesion, prevents the column falling due to gravity Water is constantly being removed from the roots into the xylem by diffusion to replace the water which has been transported upwards. Water moves into and across the root from the soil by diffusion and osmosis. Movement of water from soil to atmosphere through the plant is called the transpiration stream 4) Compare the structures, position in the stem and function of sclerenchyma fibres (support) and xylem vessels (support and transport of water and mineral ions). Strengthening cells 2 major types of elongated cells with thick, strong lignified walls and no living cell contents: Sclerenchyma and Xylem vessels Characteristics: Cellulose microfibrils run lengthways cellulose cells walls are thickened by the addition of lignin which is impregnated between the cellulose microfibrils this makes cells stiffer so less flexible and increases the tensile strength reduces the permeablity (so xylem vessels become waterproof) lignified cells are dead Sclerenchyma cells: called fibres Long, narrow cells with pointed ends to allow fibres to interlock closely (unlike xylem, they do not form tubes) Very thick lignified walls; strong and inflexible

Dead cell (no living protoplast) Principal function is support

Xylem vessels Mature xylem tubes (called vessels have no living contents (i.e. no protoplast, so dead) form hollow tubes which consist of lignified wall only so water can flow freely in lumen Xylem vessels are elongated cells; these are joined end to end with no cross walls to form long continuous tubes Wall thickened with lignin which is waterproof (so prevents water leaking out) strong (so prevents vessel collapsing) Water can pass into and out of xylem via pits (perforated holes) in the wall. Lignified walls provide support, strength and flexibility. Hollow vessels forming continuous tubes allow for the transport of water and dissolved mineral ions

5) Describe how the uses of plant fibres and starch may contribute to
sustainability, eg plant-based products to replace oil-based plastics. Plant fibres are useful to us: because fibres = bundles of sclerenchyma and xylem which can be extracted intact from plants plants from which fibres can be obtained are relatively easy to grow in quantity the fibres themselves are useful because they are long and thin, strong, flexible relatively easily and cheaply extracted, durable, resistant to decay (cellulose is difficult for decomposers to break down) Uses for plant fibres include: Clothing e.g. linen (from flax plants); Rope e.g. hemp and sisal; Sacking e.g. jute; Matting e.g. coir or coconut matting; Paper Sustainablity; Advantages of growing for fibres (e.g. nettles) a sustainable resource i.e. regrow after they are cut so no need to plant more or harvest seeds and plant those so remnants of one crop sustains the next one i.e. it is self-sustaining can be grown in poorer soils so wont use up valuable agricultural land make profitable use of marginal land use of fibres (and other plant products made from starch) replace need for oil-based plastics so reduce reliance of fossil fuels, and reduce CO2 emissions to reduce global warming natural products so biodegradable by decomposers 6) Identify sclerenchyma fibres and xylem vessels as seen through a light microscope. 7) Describe how to determine the tensile strength of plant fibres practically. Core Practical.

8) Explain the importance of water and inorganic ions (nitrate, calcium ions and magnesium ions) to plants. Inorganic ions are transported in the xylem dissolved in the water transported from root to shoot in transpiration stream Taken up by roots from soil by a combination of diffusion and active transport. Ions are the source of the elements the plants need to manufacture the complex organic molecules they need Importance of nitrate ions to plants Taken up as nitrate ion source of nitrogen atoms for making: o amino acids and proteins o DNA and RNA o component of chlorophyll molecule plants growing without nitrates are typically stunted, yellow Importance of calcium ions to plants Taken up as calcium ion; source of calcium atoms for cell walls: forms calcium pectates in middle lamella to hold cells together plants growing without calcium are typically very stunted Importance of magnesium ions to plants Taken up as magnesium ion; source of magnesium atoms for reaction centre for chlorophyll molecule plants growing without magnesium are typically yellow

9) Describe how to investigate plant mineral deficiencies practically.


Core practical: Investigation of plant mineral deficiencies. 10) Describe how to investigate the antimicrobial properties of plants. Core practical: Investigation of the antimicrobial properties of plants. 11) Compare historic drug testing with contemporary drug testing protocols, eg William Witherings digitalis soup; double blind trials; placebo; three-phased testing. Development of the use of Digitalis by William Withering in 1775 Digitalis is a natural toxin found in foxgloves (an insect antifeedant) which can be fatal in even quite small doses. But it had been used for centuries in herbal remedies to treat some heart conditions. William Withering rigorously tested digitalis and brought it into conventional medicine in 1785 as a treatment for dropsy (or congestive heart failure) which is the accumulation of fluid and swelling resulting from a weak heart: o He gave 163 Dropsy sufferers an extract of foxgloves o He increased the dosage until the patient showed signs of sideeffects (nausea, vomiting, diarrhoea and yellow/green vision - some of his patients nearly died!) o He then reduced the dosage slightly => the most effective dose o Successful treatment was that the patient survived and there was an increase in the effectiveness of the heart beat (digitoxin is a

stimulant) and an increase in urine production to remove the excess fluid What was ethically wrong with this? o An overdose of Foxglove is fatal o He gave more and more to his patients until they either showed signs of recovery or nearly died Modern drug testing Stage Pre-clinical testing Purpose of stage Proposed drug is tested in a lab with cultured cells to see the general effects of the drug Proposed drug is given to animals to see the effects on a whole animal. Any side effects away from target cells are noted. A small group of healthy volunteers are given different doses of the drug. They are told what the drug does 2.The distribution, absorbance rate, metabolism & excretion profile of the drug are assessed.3.The effects of the different doses are assessed to try and determine the optimum dose. An independent organisation (UK Medicines Control Agency) assesses whether it is appropriate to move to Phase 2 A small group of people with the disease are given the drug. Studies are very similar to Phase 1 The optimum dose is worked out A large group of people with the disease are given optimum doses of the drug [Reduces effects of chance/random variation] The patients are either given the drug or a placebo in a double-blind test [Neither patients nor doctors know who gets drug or placebo (avoids bias in looking for results) avoids patient/researcher bias in observing, recording and interpreting effects prevents subconscious prediction or influence of the outcome by both patient and researcher e.g. if know placebo used neither would expect any effect or if know drug used may feel/look for improvements that are not really there (psychosomatic influences).] The results are statistically analysed [Improves accuracy of conclusions as to whether or not drug actually does have an effect or not.] If the drug has had a significant positive and safe effect in the treatment of the disease it is put forward to licensing authority In what way is the current system of drug testing safer and more reliable than Wutherings? Safer: Use of specific active ingredient should allow a more precise dose to be given Any serious ill effects may be detected in the animal trials first

Clinical Trials Phase 1

Clinical Trials Phase 2 Clinical Trials Phase 3

More reliable: Uses larger samples reduces effects of chance/random variation Double blind testing avoids patient/researcher bias in observing, recording and interpreting effects Statistical analysis of data improves accuracy of conclusions as to whether or not drug actually does have an effect or not. 12) Explain the terms biodiversity and endemism and describe how biodiversity can be measured within a habitat using species richness and within a species using genetic diversity, eg variety of alleles in a gene pool. Biodiversity Biodiversity is the number of different species, and the number of each species in a particular area. In a community in a particular habitat the biodiversity of organisms depends on - the total number of organisms - the number of different species present = species richness - the number of organisms of each species present = species evenness So to estimate biodiversity these need to be counted or estimated using sampling techniques. - High biodiversity = high species richness (lots of different species) + high species evenness (numbers of each species roughly the same, rather than a few very common (dominant) and many very rare species) Biodiversity within a species is measured by genetic biodiversity i.e., the variety of alleles in the gene pool (by measuring the genetic differences between individuals e.g. range of genotypes and estimating the number of different alleles) Hotspots and endemism Hotspots - A biodiversity hotspot is a region with a very high biodiversity. - A hotspot is defined in terms of a region having > 1250 different pants species and must have > 0.5% of total global plant diversity present as endemic species Endemism - Endemic organisms are those found only in a specific area and nowhere else on Earth; i.e. they are unique and specifically adapted to a particular place o Endemic species are particularly vulnerable to extinction becausethey are only found in one place, so if their habitat is threatened they cant migrate and as natural selection is too slow they cant move or adapt quick enough so their numbers a likely to decline. 13) Describe the concept of niche and discuss examples of adaptation of organisms to their environment (behavioural, physiological and anatomical).

Environment:

The conditions in which an organism lives. It provides all essential resources an organism needs e.g. food, shelter, mates, nest sites, support, hiding places, suitable conditions for growth etc. Habitat: The particular place with suitable environmental conditions where an organism lives. Population: A group of individuals of the same species living and breeding together in the same habitat at the same time. Community: All the organisms of the different species living and interacting together in the same habitat. Niche The niche is the way an organism is adapted to exploit the resources of its environment so it can survive to reproduce. In simple terms it describes what a species needs to survive and what is does. Species A species is a group of similar organisms which can interbreed to produce fertile offspring. Adaptation Adaptation describes the ways in which an organism is best suited to exploit its environment. Ultimately on organisms adaptations enables it to survive to breed. Adapations can be: Anatomical An organisms structures are specifically adapted to a particular function which enables the organism to exploit its environment more efficiently Physiological An organisms physiology is adapted to survive particular conditions Behavioural Behaviour is the adaptive responses an organism makes to changes in its environment. (Use these to consider the way any organism given in a question is adapted to its niche.)

14) Describe how natural selection can lead to adaptation and evolution. In all organisms that reproduce sexually, every individual has its own unique genotype i.e. combination of the alleles of all its genes: this is genetic diversity. Genetic diversity describes the number of different combination of alleles (i.e. genotypes) within the gene pool of a population of a species. All the alleles of all the genes in all the organisms in a population is called the GENE POOL. The greater the number of alleles in the gene pool the greater the number of genotypes in a population, so the greater the genetic diversity. Sources of variation Mutations - produces new alleles i.e. new versions of genes

Meiosis - mixes up combinations of alleles of all the genes to produce different genotypes by crossing-over and independent assortment

What is the significance of genetic diversity? It enables populations of organisms to become adapted to changes in the environment over time by natural selection. Natural selection Learn the wording! It can be applied to any situation given in a question.

pool of population) so individuals in populations have different genotypes and show genetic variation If there is a change in the environment some genotypes with particular alleles may now make some organisms more likely to survive long enough to reproduce, to pass these genes on to their offspring i.e. they are better adapted to their environment. Others less well adapted will die from predation, competition for food, disease etc. Those that reproduce will have offspring, some of which will inherit the favourable genotype and so themselves are more likely to survive to breed to pass their genes on Over time the proportion of individuals with the favourable alleles in their genotype will increase in the population NB: This can only happen if an advantageous allele of a gene already exists 15) Discuss the process and importance of critical evaluation of new data by the scientific community, which leads to new taxonomic groupings (ie three domains based on molecular phylogeny). Each species has its own individual and unique name which is internationally recognised. All organisms have a specific and unique biological name which all scientists use to avoid confusion; they are named using a universal scientific system known as the Binomial system, i.e. the binomial name consists of two parts.

Random mutations produce new variation (they add new alleles to gene

Biological identification

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To be able to estimate biodiversity we need to be able to recognise and name individual species accurately. One way of doing this is to use a branching or dichotomous identification key. This uses pairs of particular characteristic features in a step-wise sequence which ultimately leads to the name of the particular species. Modern keys are computer-based quicker, allow multiple access and easily updated as new species are discovered

Why might identification keys not work? - Particular features required in the key may be absent because: o damage to specimen o wrong stage of development (e.g. very young) o previously unknown species - Characteristics used are difficult to identify or interpret - Rare species may not be included Organisation of biodiversity: Biological classification. Why are organisms classified? To produce a universal 'filing system' to put groups of similar organisms together. To show evolutionary relationships To allow identification of different species and to give them a formal name To allow the recognition of new species Allows us to catalogue biodiversity (i.e. recognise and count the numbers of different species) To allow predictions to be made about individual members of a group, e.g. if a particular plant produces medicinal chemicals it is likely that other members of the same group will also do so. To show evolutionary relationships Features used in classification Those that are easy to see/measure Those that do not change Those that are present in all members of a group How are organisms classified? Classification puts organisms into groups where all the members of one group resemble each other (share more common features) more than they do members of other groups.

Organisms are grouped together to reflect evolutionary relationships


because they share common ancestors. So all the organisms in one group are more closely related to each other than to members of other groups.

Five Kingdom system of classification. The Kingdoms are: Prokaryotae Protoctista Fungi Plantae Animalia. (Learn three diagnostic features for each Kingdom.) Prokaryotae (Bacteria and blue-green bacteria) Cells are prokaryotic (no nucleus, no organelles) and very small (< 10 mm) Cell walls made of petidoglycan (not cellulose) Protoctista Autotrophic i.e. photosynthetic (e.g. seaweeds) and heterotrophic (feed on ready made food) (e.g. Plasmodium) Eukaryotic; unicellular and multicellular (but limited differentiation into tissues, organs etc). (Organisms are classed here if they do not fit into any other Kingdom) Fungi Unicellular or multicellular eukaryotes Heterotrophic absorb food, either as a result of external digestion (=decay) or as parasites Some unicellular (e.g. yeasts) but usually body is a multicellular (but often no separate cells, so more accurately multinucleate)) mass (mycelium) of thread-like filaments (hyphae) Cell walls made of chitin Plantae Multicellular eukatyotes Complex body structures; specialised cells, tissues, organs Cell walls made of cellulose Autotrophic (make their own food by photosynthesis); contain chlorophyll Animalia Multicellular eukaryotes Complex body structures; specialised cells, tissues, organs

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Heterotrophic; most have a gut (digestive system) Cells lack cell walls Most are motile (but not all). Have a nervous system

Three Domains Modern evidence based on DNA and RNA suggests the Kingdom Prokaryotae should be divided into two separate Domains the Archea (ancient bacteria found in extreme environments) the Eubacteria (all the other bacteria). All the eukaryotic organisms are found in the Domain Eucarya, so there are 3 Domains of living organisms: Archea, Eubacteria, Eucarya. 16) Discuss and evaluate the methods used by zoos and seedbanks in the conservation of endangered species and their genetic diversity (eg scientific research, captive breeding programmes, reintroduction programmes and education). Organisms could become endangered or extinct in the wild if: Loss of habitat or habitat fragmentation from deforestation, loss of hedgerows etc.,or reduction in numbers from pollution, poaching, shooting, loss of prey species to feed on etc reduces the sizes of populations They will become endangered or extinct if remaining organisms are unable to adapt rapidly enough to a rapidly changing environment, or are unable to breed and produce sufficient new viable offspring to replace the ones that die (due to genetic drift or inbreeding and loss of vigour). This results in a loss of biodiversity Conservation is a way of maintaining the diversity of habitats and the living organisms that live there to prevent them from disappearing. One of the ways vulnerable populations of endangered species can be supported so they do not become extinct in the wild is by the conservation work carried out by zoos (for animals) and seed banks (for plants) Zoos provide for Academic research Education Captive breeding Reintroduction programmes

Zoos and captive breeding programmes Aims of captive breeding programmes: To increase the number of individuals of a species if numbers are low To maintain genetic diversity within the captive population To reintroduce animals into the wild if possible

Problems facing captive breeding programmes for the maintenance of genetic diversity: Small populations tend to become genetically uniform because variation and genetic diversity is lost so all individuals have similar genotypes because of genetic drift and inbreeding depression

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Many genetic diseases are caused by harmful recessive alleles and their frequency will increase in an increasingly homozygous population leading to a loss of vigour, lower disease resistance, and less ability to survive and adapt to a changing environment. This is inbreeding depression. Summary: Genetic drift in a small breeding population is the random loss of alleles from the gene pool which reduces the amount of genetic diversity Inbreeding depression

Inbreedin

In a small pop

is the result of closely related animals mating in a small population leading to a reduction in the number of heterozygous individuals and an increase in the number of homozygous individuals which reduces the range of genotypes in subsequent generations, and the expression of harmful recessive alleles leads to a reduction in viability.

Both reduce genetic diversity; population becomes more uniform The maintenance of genetic diversity A wide range of different genotypes within populations of organisms is essential to enable natural selection to operate on this range of genotypes to maintain populations of organisms adapted to the environment of the time but also to maintain sufficient variation to allow for selection to cope with any changes in the environment it also ensures captive organisms are still genetically similar to wild populations so successful breeding between wild and introduced animals can occur How genetic diversity is maintained in zoos and captive breeding programmes. Zoo sets up a breeding programme with its captive animals Mates are carefully selected Individual animals are only allowed to mate with unrelated individuals (can be checked by use of DNA profiling genetic testing), and different mates to any previous matings so only animals with different genotypes are allowed to mate to increase genetic diversity Genetic diversity can be further increased by using animals from other zoo populations or animals captured in the wild This is monitored by the use of studbooks basically, this is a family tree for the captive animals are kept so that only non-related animals (often determined by analysis of their DNA) are bred with each other. this decreases the chance of genetic drift and inbreeding depression Captured wild animals are introduced to mate with animals in captive populations (this is called out-breeding) these will have with new genotypes (i.e. combinations of the alleles of all the genes) the animals can introduce new alleles or reintroduce alleles to replace those lost as captive animals die this can increase the size of gene pool (i.e. more different alleles) so more variation ensure captive animals remain heterozygous so recessive alleles are not expressed

Summary Stud books and the introduction of captured wild animals ensures the captive breeding population remains heterozygous so decreases the chance of loss of genetic diversity due to: genetic drift and inbreeding depression Reintroducing zoo-bred animals into the wild Reintroducing species into the wild has some success, but depends greatly on the species. As a general rule of thumb, the more advanced the species the more difficult reintroduction is. This is because animals need to learn specific behaviours e.g. how to hunt, how to reproduce, how / where to find shelter, group behaviours: if they cant do this because of their experience of the zoo environment reintroduction is unlikely to be successful Breeding animals in captive environments that mimic the wild has more success because it allows some of these behaviours to be learned in captivity. Feeding the animals in the wild also helps survival rates e.g. orang-utan reintroduction programmes in Borneo. There is a remote risk that re-introduced animals may bring in a new disease which they may be immune to but the wild populations are not Seed Banks Millennium Seed Bank Project Conservation of plants is important too because plants are: Endangered from habitat destruction, climate change, agriculture Potential sources of new medicines, New plants for food and other products Sources of genes for plant improvement etc Seed Banks: Seed samples (seeds contain genes!) from tens of thousands of different species are kept in seed banks; some in their countries of origin, and many in the Millenium Seed Bank Project run by Kew Gardens. Initially set up to collect and store seeds from all the UK native species. Another aim is to conserve 10% of the world flora, particularly focussing on those most threatened with extinction. At the MSP: Seeds collected, identified, cleaned and dried screened using x-rays to check they have fully developed embryos (so are viable) stored in cool (-20oC) and dry conditions (so dont germinate) so can be stored for a long time tests carried out at regular intervals to check seeds are still viable (i.e. will still germinate and grow) if evidence shows viability is reducing some seeds are sacrificed to be grown into plants, allowed to flower and cross-pollinate to produce seeds; the seeds are then collected and stored again.

Advantages of using storing seeds as the source of genes: Less space needed/less costly and less labour intensive to store large numbers of seeds than whole plants Seeds can all be stored in same environment, whereas whole plants need different and specific conditions to much easier to maintain Seeds less likely to be eaten by herbivores/killed by disease than whole plants Enables a large stock of the genetic variation of the wild populations to be conserved (especially if the plants are endangered in the wild) for possible future use in plant breeding programmes. Can also be used as a source of plants for re-introductions back into the wild. Most plants produce many seeds so collecting seeds is unlikely to seriously harm the numbers of plants in a vulnerable population Seeds are easily transported Seeds do not need to be stored in original habitat and are so less likely to damaged by vandalism, pollution, disease, grazing or natural disasters

Some plants do not produce many seeds, or produce non-viable seeds, so their genomes need to be stored in different ways e.g. as callus in tissue culture stored at very low temperatures (cryopreservation), or as the plants themselves growing in field gene banks e.g. used to store thousands of different cloned varieties of potato in Peru or rice in the Philippines.