Classification and evolution Taxonomic groups = hierarchial groups in classification Kingdom, Phylum, Class. Order, Family, Genus, Species Recently, scientists have added another kingdom and 3 domains Why use it? identify species predict characteristics find evolutionary links Binomical nomenclature --> Genus species (Canis familiaris) Five kingdoms Prokaryotae --> bacteria unicellular  no nucleus or membrane-bound organelles circular DNA no visible feeding mechanism Protoctista --> amoeba mostly unicellular nucleus and membrane-bound organelles are present some have chloroplasts some have cilia or flagella Fungi --> mushrooms, moulds or yeast unicellular or multicellular nucleus and membrane-bound organelles are present cell wall = chitin no chloroplasts nutrients acquired from dead or decaying material Plantae  multicellular nucleus, membrane-bound organelles and chloroplasts present gametes move with cilia or flagella autotrophic feeders cell wall = cellulose food stored as starch Animalia  multicellular nucleus and membrane-bound organelles present no chloroplasts or cell walls hetereotrophic feeders food stored as glycogen Evolutionary relationships as they become different their DNA changes so their proteins and sequence of amino acids also change The 3 domains Based on differences in the sequence of nucleotides in rRNA and the cell membrane lipid structures  and sensitivity to antibiotics Eukarya 80S ribosomes RNA polymerase has 12 proteins Archaea 70S ribosomes RNA polymerase has 8-10 proteins Bacteria 70S ribosomes RNA polymerase has 5 proteins Under this system, the Prokaryotae kindgom is split into Archaebacteria and Eubacteria Archaebacteria "ancient" bacteria live in extremes like thermal vents Eubacteria "true" bacteria found in all environments Phylogeny = evolutionary relationships between organisms Phylogenetic trees show the relationships with branches from the common ancestor relies on physical characteristics and genetic makeup can be done without reference to classification continuous tree --> no groups means there's no species that there's debate over where they belong  Evidence for evolution Palaentology --> study of fossils bacteria in the oldest rocks and invertebrates and vertebrates in the more recent ones which supports evolution because there's time between the lesser and more complex organisms sequence in which organisms are found matches with ecological links (plants older than animals) similarities in anatomy of fossils shows how closely related organisms  evolved from common ancestor BUT fossil record isn't complete Comparative anatomy --> similarities and differences in the anatomy of organisms used because the fossil record isn't complete homologous structure = structure that appears superficially different in different organisms or has a different function provides evidence for divergent evolution (species have evolved from a common ancestor into different forms) Comparative biochemistry --> similarities and differences in the proteins and other essential molecules some molecules are highly conserved so changes can show evolutionary links mostly study cytochrome c (protein in respiration) or rRNA neutral evolution = most of the variability of the molecule occurs outside of its functional region so accumulation isn't affected by natural selection therefore changes to these regions can show how close two species are the number of differences between a molecule is plotted against the rate at which the molecule undergoes neutral base pair substitutions so a point can be estimated where they last shared a common ancestor rRNA is used because it has a slow rate of substitution  Variation interspecific variation = variation between members of different species intraspecific variation = variation between members of the same species causes = genetic or environmental Genetic variation alleles  mutations meiosis --> independent assortment and crossing over sexual reproduction chance Environmental variation plants are more affected than animals because they cannot move sunlight water availability scars on the skin Both tall parents --> you have the alleles to be tall but if your diet isn't right or you suffer from a disease, it means you may grow below average height skin colour --> determined by melanin in your skin, birth skin colour is purely genetic but the more you're exposed to sunlight, the concentrations of melanin change  Discontinuous variation = when variation can only result in certain values --> blood type and bacterial cell shape (spherical, rods, spiral, comma or corkscrew) controlled by a single gene represented in a pie chart or bar chart Continuous variation = when variation can be any value within a range --> height, mass controlled by more than one gene as well as environmental factors represented in line graphs or histograms Normal distribution = bell-shaped curve mean, mode and median are all the same distribution is bell shaped or symmetrical around the mean 50% are less than the mean and 50% are more than the mean most values lie close to the mean Standard deviation = how spread out the data is Greater the SD, the greater the spread Characteristic with a high SD has a large amount of variation normal spread = 68% within 1 SD, 95% within 2 SD, 99.7% within 3 SD Student's t test = compare the mean values of two sets of data the data must be normally distributed and there muse be enough data to calculate a reliable mean Spearman's rank correlation coefficient = used to consider the relationship between two sets of data no correlation = no relationship negative correlation = as one set increases, the other decreases positive correlation = as  one set increases, so does the other Adaptations Anatomical adaptations = physical features body covering = hair, scales, spines, feathers, shells to stay warm or protect them camouflage = outer colour blends into environment to make it harder to predators or prey to spot you teeth = shape and type are related to diet mimicry = copying another animal's appearance or sounds to allow a harmless animal to fool predators Marram grass --> curled leaves to minimise the surface area, hairs on inside surface area of the leaves to trap moist air, sunken stomata, thick waxy cuticle Behavioural adaptations = the way the organism acts survival behaviours = opossums play dead courtship = elaborate courtship rituals to attract a mate seasonal behaviour = migration to nesting sites or hibernation through the winter innate = inherited through genes, doesn't have to be learned learned = adaptations learned from observing other animals Physiological adaptations = processes that take place inside the animal poison production  antibiotic production water holding  Anatomical adaptations provide evidence for convergent evolution analogous structure = adapted to perform the same function but have a different genetic origin convergent evolution takes place when unrelated species begin to share similar traits these are due to them evolving in similar environments marsupial and placental mice - both are small and agile climbers that forage at night for small food items flying phalangers and flying squirrels - both are gliders that eat insects and plants marsupial and plancental moles - both burrow to find worms and grubs, they have streamlined bodies Natural selection organisms within a species show genetic variation organisms who are best adapted to a selection pressure have an increased chance of survival and successfully reproducing --> survival of the fittest successful organisms pass on the allele encoding for the advantageous characteristic the process is repeated for each generation so over time the proportion of individuals with the advantageous allele increases in the gene pool over a long time the process can lead to speciation Modern examples of evolution  antibiotic-resistant bacteria --> MRSA peppered moths --> industrial revolution meant that the black ones became camouflaged where the white ones didn't sheep blowflies became resistant to the pesticide used against them falvobacterium has evolved to digest nylon which is beneficial to humans as it clears up factory waste (developed nylonases due to gene replication combined with frameshift)

Biodiversity Importance = essential for maintaining a balanced ecosystem for all organisms --> they provide food, oxygen and other materials for us to survive Measuring a baseline for the biodiversity of an area means you can work out how much of an effect a change has had/ will have on the area Habitat biodiversity = number of different habitats found within an area each habitat will have different numbers of different species so the higher the habitat diversity the higher the biodiversity Species biodiversity has two compononents: ​​​​​​​species richness --> number of different species living in a particular area species evenness --> comparison of the number of individuals of each species in a community overall species diversity can be different even if it has the same number of species, it also depends on the evenness Genetic biodiversity = variety of genes that make up a species many of the genes are the same for all individuals in the species but alleles do exist and they cause the genetic variation within and between species genetic biodiversity can result in different characteristics being exhibited (dogs can be big or small, round or pointy eared)  greater genetic biodiversity within a species allows for better adaptation to a changing environment Sampling = taking measurements of a limited number of individual organisms within a particular area Used to estimate the number of organisms in an area aka the abundance of the organisms Also used to measure a particular characteristic of an organism (average height of crop) Random sampling = selecting individuals by chance each population has equal chance of being recorded mark out a grid on the grass using tape measures use random numbers to determine coordinates take a sample from each randomly generated coordinte pair Non-random sampling = sample is not chosen at random opportunistic --> weakest form of sampling as it is not representative of the whole population (uses organisms that are conveniently available) stratified --> some population can be divided into sub-groups based on a particular characteristic, a random sample is then taken from each of the groups proportional to its size systematic --> areas are identified within a habitat that are then sampled separately --> usually with line (line along the ground and take samples from specified points) or belt transect (two parallel lines marked and samples taken in the area between them) Reliability Sample is never entirely representative because: sampling bias --> may be by accident or deliberate (you choose an area because you know it'll give you good numbers for certain species) chance --> the organisms selected may not be representative of the whole population --> can never be removed but its effects can be minimised with large sample sizes  Sampling animals pooter to catch insects sweep nets to catch insects in long grass pitfall traps for small invertebrates tree beating for invertebrates that live in trees or bushes (shake it over a white cloth to catch them) kick sampling for organisms in a river (the riverbed is "kicked" for a while before to disturb the substrate then a net catches anything that's disturbed downstream) Estimating animal population size capture-mark-release-recapture technique capture as many as you can mark them all and then release them time is allowed for the organisms to redistribute themselves repeat the capture process and compare the numbers that are new or recaptured the greater the marked individuals recaptured the smaller the population size Sampling plants point quadrat --> frame with a horizontal bar, at set intervals a pin is pushed through to the soil and each plant that touches the pin is recorded frame quadrat --> sqaure frame divided into a grid, the type and number of species and individuals within each section is recorded used to measure: density --> if plants can be seen clearly, counting how many are in one quadrat shows the density of the plant per metre <-- not an estimate frequency --> used where individuals of a species are hard to count --> count the number of squares the species is present within to work out an estimated percentage (clover in 65 of 100 squares means they are in 65% of the area) percentage cover --> used for speed when collecting data --> used when a species is abundant but hard to count --> estimate by eye of the area within the quadrat that the plant is present within for best results, quadrats should be used in random sampling but often aren't) Measuring species richness make a list of all the species identified then a total number can be calculated identification keys are used when sampling Measuring species evenness compare the numbers for the individuals in each species Measuring abiotic factors abiotic factors = non living components in a habitat wind speed light intensity --> light meter relative humidity --> humidity sensor pH --> pH probe temperature --> temperature probe oxygen content of water --> dissolved oxygen probe can be measured quickly and accurately so that: rapid changes can be detected human error in taking reading is reduced high degree of precision data can be stored and tracked Calculating biodiversity use the Simpson's Index of Diversity to take both species evenness and richness into account values always between 1 and 0 --> closer to 1 means higher biodiversity organisms in a low biodiversity habitat are usually highly adapted to survive there Genetic diodiversity differences in alleles create genetic biodiversity species with greater genetic biodiversity are more likely to adapt and survive as it is likely that some organisms carry the advantageous alleles increased by: mutations in the DNA interbreeding between different populations as the alleles are transferred between the groups aka gene flow decreased by: selective breeding where organisms are only selected to breed if they have desirable traits captive breeding programmes in zoos and conservation centres as new alleles are rarely introduced rare breed where they have been selectively bred but then go out of fashion so numbers and allele numbers drop dramatically artificial cloning natural selection --> organisms evolve to only carry the advantageous alleles genetic bottlenecks --> few individuals survive an event or change so the gene pool is reduced genetic drift due to random nature of alleles being passed from parent to offspring (more pronounced in populations with small gene pools) Measuring genetic biodiversity measure polymorphism (polymorphic genes have more than one allele like immunoglobulin which codes for blood type) most genes are monomorphic where only a single allele exists (ensure the basic stucture of a species stays the same) proportion of genes that polymorphic can be measured by: number of polymorphic gene loci / total number of loci the greater the proportion of polymorphic genes, the greater the genetic biodiversity in a population Factors affecting biodiversity deforestation can occur naturally but it is mostly deliberate by humans affects biodiversity by: directly reduces the number of trees in an area specific species are sometimes targeted so it reduces species biodiversity destroys the habitats for animals so their numbers fall too animals are forced to migrate to ensure their survival agriculture  selection of only a few species reduces the biodiversity of the area much of the methods used by farmers reduces biodiversity: deforestation to create area for planting  removal of hedgerows use of pesticides and herbicides monoculture  climate change and global warming melting of the polar ice caps would lead to the extinction of the plants and animals in these regions rising sea levels from the melting caps and thermal expansion of the seas would lead to flooding higher temperatures and less rainfall would result in droughts and some plant species dying out + xerophytes would become more dominant --> less food for some animals so the ones who eat xerophytes would be more common insect life cycles and populations would change as they adapt to the new climates --> as key pollinators they would effect the plants as well slow climate change would give time for species to adapt and as this would lead to the loss of native species, biodiversity wouldn't be lost Reasons for maintaining biodiversity aesthetic reasons: different plants and animals enrich out environments and lives natural world provides inspiration for the arts patients recover more quickly from stress if they're surrounded by plants economic reasons: soil erosion may occur as a consequence of deforestation so there would be a drop in land available for crops and animals important to conserve the organisms we use to make things (hardwood timber) to prevent industries breaking down protect species with potential economic importance --> undiscovered medicines continuous monoculture depletes the soil which would lead to smaller crop yields and less money high biodiversity protects against abiotic stresses so crops are more likely to survive economic income from areas of natural beauty plant varieties are needed for cross-breeding to make more profitable and successful crops ecological reasons: the removal of one species could have a serious effect on the others in its ecosystem - including us! keystone species have a disproportionally large effect on their environments so its essential to protect them so other species don't also disappear Human activity vs biodiversity in many countries the natural habitat is created and maintained by human intervention by farmers and landowners Maintaining biodiversity In situ conservation = within the natural environment maintains the genetic diversity and the evolutionary adaptations preserves interdependent relationships therefore interlinked species are also protected wildlife reserves: controlled grazing restricted human access controlling poaching feeding animals reintroduction of a species removal of invasive species halting succession marine conservation zones: less well established vital in preserving species-rich areas aim is to create areas of refuge where populations can build up and repopulate adjacent areas Ex situ conservation = outside of the natural environment botanic gardens: plant species actively maintained to provide optimum conditions roughly 1500 worldwide holding 35,000 plant species majority of species aren't conserved though many wild species are unrepresented seed banks: store of genetic material seeds are carefully stored so new plants can be grown in the future dried and stored at -20C don't work for all plants, some seeds die when dried and frozen (mostly the seeds from rainforests) captive breeding programmes: often run and managed by zoos and aquatic centres scientists help to create a stable, healthy population of the species so it can be gradually reintroduced to its natural habitat provide the animals with shelter, food, no predators and vets suitable breeding partners or semen can be imported from other zoos to increase the gene pool maintaining genetic biodiversity can be difficult as interbreeding happens often sometimes they cant't be reintroduced because: loss or resistance to a disease may not have learned the correct behaviours to survive genetic make up of the captive species may be too different from wild ones in many cases the natural habitat must first be restored conservations agreements International Union for Conservation of Nature (IUCN) assist in securing agreements between nations established the Convention of International Trade in Endangered Species (CITES) which regulates the trade of wild plant and animal specimens (protects 35,000 species) the Rio Convention of 1992 --> 172 nations agreed on : Convention of Biological Diversity (CBD) requires them to develop national strategies for sustainable development United Nations Framework Convention on Climate Change (UNFCCC) agreed to take steps to stabilise greeenhouse gases United Nations Convention to Combat Desertification (UNCCD) aims to prevent desertification of fertile land

Communicable diseases Types of pathogen bacteria prokaryotes classified by shape: rod = bacilli spherical = cocci comma shaped = vibrios spiralled = spirilla corkscrew = spirochaetes classified by cell walls and how they appear after gram staining: gram positive bacteria = purple-blue under light microscope --> MRSA gram negative bacteria = red under light microscope --> E.coli useful because it effects how they react to antibiotics viruses non-living infectious agents some genetic material surrounded by protein they invade living cells, hijack the biochemistry and make more virsuses reproduce rapidly and evolve by developing adaptations to their host there are even ones that attack bacteria called bacteriophages considered ultimate parasites proctoctista (protista) eukaryotic microorganisms with various feeding methods percentage act as pathogens for both plants and animals --> parasitic many need a vector to transfer them or they may enter the body through contaminated water fungi cause more devastation in plants eukaroyitc organisms but the ones that effect humans tend to be single-celled some are parasitic and feed on living plants and animals normally stop plants from photosynthesising Modes of action damaging the host tissues directly viruses take over cell metabolism --> make host cell create loads of copies of them then they burst out which destroys the cell some protoctista take over cells but don't take over genetic material they just digest the cell's contents when they reproduce fungi digest living cells and destroy them  producing toxins most bacteria produce toxins that poison or damage host cells --> breakdown the membranes, inactivate enzymes or interfere with genetic material some fungi produce toxins Plant diseases ring rot effects tomatoes, potatoes and aubergines caused by gram positive bacteria damages leaves, tubers and fruit tobacco mosaic virus effects tobacco plants, tomatoes, peppers and cucumbers caused by virus damages leaves, flowers and fruit  potato blight effects potatoes and tomatoes caused by protoctist  destroys leaves, tubers and fruit no cure black sigatoka effects bananas caused by fungus penetrates and digests cells can cause 50% reduction in yield no cure Animal diseases tuberculosis bacterial disease damages lung tissue and suppresses immune system both curable and preventable in humans bacterial meningitis  bacterial infection of meninges of the brain which can spread to the rest of the body mainly effects young children and teenagers antibiotics cure it if given early enough vaccines prevent it HIV/AIDS acquired immunodeficiency syndrome caused by human immunodeficiency virus HIV targets T cells in immune system gradually destroys immune system so people infected are open to other diseases (TB or pneumonia)  HIV = retrovirus so infects the host cell, uses reverse transcriptase to make DNA from its own RNA which interacts with the host's DNA passed through bodily fluids  no vaccine and no cure anti-retroviral drugs slow the process Influenza viral infection of ciliated epithelial cells in the gas exchange system (kills them which opens the airways to secondary infection) three main strains - A, B & C strain A are the most virulent and classified further by proteins on their surfaces mutate regularly  vaccines available every year with the predicted variations no cure Malaria protoctista spread by bites of mosquitoes female mosquitoes bite for blood to get protein before she lays her eggs the protoctista invades the red blood cells, liver and brain the disease recurs making them weak and vulnerable no vaccine and limited cures need to control the vector / mosquitoes Ring worm fungus affecting mammals not damaging, just looks unsightly and is itchy antifungal creams clear it Athlete's foot human fungal disease form of ring worm that digests the skin between the toes antifungal creams cure it Transmission of pathogens between animals direct transmission direct contact (kissing, skin-to-skin contact, microorganisms from faeces transmitted on the hands) inoculation (break in the skin, bite, puncture wound) ingestion (contaminated food or drink) indirect transmission fomites (inanimate objects like bedding, socks or cosmetics) inhalation (droplets of saliva or mucus from coughing, speaking or sneezing)  vectors (transfer communicable pathogens unintentionally)  water acts as a vector factors affecting transmission overcrowded conditions poor nutrition compromised immune system poor waste disposal climate change can introduce new vectors and pathogens culture and infrastructure socioeconomic factors like a lack of trained health workers Transmission of pathogens between plants direct transmission contact of healthy plant with infected one indirect transmission soil contamination (could leave reproductive spores in soil that infect next crop) vectors (wind - may carry any pathogen, water - spores float on the surface, animals - insects and birds carry pathogens and spores as they feed, humans - transmitted by contact) factors affecting transmission some vareities are suceptible to diseases overcrowding increases contact poor nutrition reduces resistance damp, warm conditions increase the survival of pathogens climate change - increased rainfall and wind promote the spread of pathogens Plant defences against pathogens recognising an attack receptors in cells respond to molecules from the pathogens or chemical produced when cell wall is attacked stimulates signalling molecules which trigger responses like production of defensive chemicals, sending alarm signals to uninfected cells and physically strengthen the cell walls physical defences callose is synthesised and deposited in the cell walls and membranes to act as barriers around site of infection large amounts of callose continue to be deposited in the cell walls and lignin is added to make the barrier thicker and stronger callose blocks sieve plates of phloem to cut off infected region callose is deposited in plasmodesmata to seal the cell off from healthy cells chemical defences insect repellents insecticides antibacterial compounds containing antibodies antifungal compounds with chitinases which interfere with fungi membranes anti-oomycetes with glucanases which breakdown glucans found in cell walls of oomycetes general toxins Non-specific animal defences skin - produces sebum, an oily substance than inhibits the growth of pathogens most body tracts are line by mucous membranes that secrete mucus to trap microorganisms (also contains lysozymes and phagocytes) tears, stomach acid and urine contain lysozymes expulsive reflexes (coughing and sneezing)  blood clotting platelets come into contact with collagen in skin or blood vessel walls platelets adhere and secrete thromboplastin and sertonin thromoplastin catalyses the production of thrombin which catalyses the production of fibrin which forms the clot sertonin causes vasoconstriction to reduce blood flow to the area scars from when to much collagen is used to stitch the wound back up inflammatory response mast cells are activated by damaged tissue mast cells release cytokines and histamines cytokines attract white blood cells to the site histamines cause vasodilation to increase the temperature (stops pathogen reproduction) and increases the permeability of blood vessels so the increased tissue fluid is used to restrict the pathogen fevers high temperatures inhibit pathogen reproduction specific immune system works faster at higher temperatures phagocytosis pathogens produce chemicals that attract phagocytes they recognise the pathogen's antigens as non-self they engluf the pathogen and enclose it in a phagosome the phagosome then fuses with a lysosome to make a phagolysosome the enzymes in the lysosome digest the pathogen when a macrophage englulfs a pathogen it combines the antigens with its MHCs (major histocompatibility complexes) aka special glycoproteins in its plasma membrane --> forms a APC (antigen-presenting cell) which stimulates the specific response helpful chemicals cytokines cell-signal other phagocytes into helping out in the infected region + increase the body temperature opsonins bind to pathogens to tag them for phagocytes (bind to protein in the phagocytes membranes) Specific immune response antibodies Y shaped glycoproteins aka immunoglobulins that bind to a specific antigen or toxin two identical long heavy chains bound to two identical short light chains with disulfide bridges the binding site is at the end of the light chains aka the variable region rest of the atibody is the same on all of them so = constant region the hinge region where the heavy binds to light chains gives it flexibility to bind to two antigens at once forms antibody-antigen complexes they help by: complex acts as an opsonin most pathogens are no longer effective when its bound to antigens act as agglutinins which clump pathogens together act as anti0-toxins lymphocytes T helper cells --> have receptors on their membranes that bind to the antigens on the APCs; they produce interleukins (type of cytokine) which stimulate the activity of B cells T killer cells --> destroy pathogens with perforin which increases their membrane permeability so the pathogen cell leaks  T memory cells --> part of the immunological memory (when they meet the pathogen again they quickly divide and handle it fast) T regulatory cells --> suppress the immune system to control and regulate it Plasma cells --> produce antibodies for the particular antigen B effector cells --> divide to form plasma cell clones B memory cells --> part of the immunological memory (remember specific antibody needed for that antigen) cell mediated immunity phagocyte englufs pathogen to become an APC receptors on T helper cells fit the antigen T helper cell is the replicates by clonal expansion --> the clones differentiate into T helpers, T killers, T regulatory cells, and T memory cells --> also releases interleukins to stimulate more phagocytosis humoral immunity APCs = B cells interleukins produced by the activated T helper cell attracts B effector cells B cells have antibodies in their membrane - when the right antibody binds to the antigen on the APC it undergoes clonal expansion clonal expansion of B cell results in plasma cells and B memory cells plasma cells release a load of antibodies into the blood to help fight the infection Autoimmune diseases = when the T regulatory cells don't work properly so the immune system continues its attack but on self cells type 1 diabetes, arthritis, lupus Natural immunity active = when the body itself acts to produce antibodies and memory cells passive = breast feeding passes antibodies from mother to baby *first milk is most important aka colostrum* Artificial immunity active = vaccinations (prevent epidemics) passive = antibody injections Medicines and the management of diseases sources of medicines penicillin comes from a mould scientists design drugs on complex comupter programmes analysis of the genomes of pathogens to find vulnerabilities Drug design for the future pharmacogenetics personalised medicine where the drugs work with your individual combination of genetics and disease (look at genome of patient and genome of pathogen) synthetic biology using genetic engineering we can develop populations of bacteria that produces drugs that are otherwise very rare, too expensive or not available mammals also used to produce drugs in their milk (pharming) nanotechnology uses tiny non-natural particles that are used for biological purposes The antibiotic dilemma antibiotics work through selective toxicity where bacterial cells but not body cells are affected over-prescriptions of antibiotics mean that some bacteria have built up resistance to the, antibiotic resistant bacteria include MRSA and C. difficile which cause real issues in hospitals and care homes antibiotic resistance can be reduce long-term by: minimising the use of antibiotics ensuring every course is completed fully good hygiene in care homes, hospitals and in general