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Biology Unit 4 revision summary of processes Photosynthesis Photolysis decomposes H2O to O2, e- and H+ O2 air as waste product e- PS2 to PS1 (via electron chain, energy released to transport protons into thylakoid membrane, the concentration gradient causes protons to be released back into the stroma generating energy which adds phosphate to adenine diphosphate generating ATP) H+ used to reduce NADP (with electron from PS1) Calvin cycle RuBP (+CO2) > RUBISCO > GP [NADP+ATP] > GALP > GLUCOSE / RuBP Primary Succession Landslide / volcano Empty inorganic surface bare rock / sand dune Pioneer species algae/moss Penetrate surface break it down into grains Organic material becomes trapped breaks down into humus Humus + rock grains = soil Grass/ferns can develop root systems die and add to soil Larger plants can survive due to newer soil layers more water/nutrients stored Plant/animal biodiversity increases until climax community Secondary Succession Fire/flood Existing soil Plants/animals present Increase in diversity until climax community Experiment: Ecology Random sample avoid bias [use water boatman from pond] Frame quadrat / point quadrat populations Line transect / belt transect / interrupted transect Abiotic/biotic factors - measured Repeat for reliability Evolution 1) Individuals within a population show variation in their phenotypes 2) Predation disease and competition create a struggle for survival. 3) Individuals with better adaptations are more likely to survive reproduce and pass on their advantageous adaptations to their offspring. 4) Over time, the number of individuals with the adaptations increases so over generations the adaptations become more common in the population through evolution. Rigor mortis Oxygen not being transferred throughout body Lack of oxygen in cells leads to anaerobic respiration ATP is used, lactic acid is produced Acid reduces pH denatures enzymes - muscles stay contracted rigor mortis Bonds between muscle proteins become fixed. Lysosomes eventually break down cells

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Insect succession Colonisers anaerobic bacteria (from the gut) spread over body Blowflies lay eggs in bed / feed on tissue Beetles eat maggots Parasitic wasps lay eggs in fly/beetle larvae Entomology life cycle Blowflies lay eggs in corpses (in orifices / wounds) maggots hatch and feed on body until they form a pupa new adult fly hatches Based on what stage of the life cycle the blowflies are at determine time of death Higher temperatures decrease in the length of life cycle. Experiment: effect of temperature on organism (brine shrimp) 1) Determine range of temperatures to be used 2) Add sea salt to beaker 3) Add de-chlorinated water and stir until salt dissolves 4) Place brine shrimp egg cysts onto paper 5) place paper into beaker 6) Incubate the beakers at different temperatures controlling extraneous variables 7) Each day use a light source to attract the larvae and count how many there are. 8) Evaluate any ethical issues that can arrive from using living organisms. Protein synthesis Transcription (nucleus) DNA hydrogen bonds broken down by RNA polymerase DNA template strand is transcribed to complementary mRNA antisense strand (formed with RNA polymerase) Thymine is replaced with uracil mRNA passes through pores in the nuclear membranes to cytoplasm then to surface of ribsomes Translation (cytoplasm / ribosomes) tRNA carries anticodon carried to surface of ribosome Each strand on mRNA has a start codon / stop codon mRNA becomes attached to ribosome reads at the start codon tRNA carries amino acids to the surface of the ribosome lining up its anticodon against a complementary codon on the mRNA Hydrogen bonds between tRNA and the ribosome bind it in place while enzymes link amino acids together with peptide bonds forming proteins tRNA finishes and returns to cytoplasm for more amino acids

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Experiment: Gel electrophoresis DNA divided into fragments using restriction endonuclease Gel electrophoresis chromatography DNA fragments- agarose gel (containing dye that will be apparent under UV / buffer / known DNA fragments) Electric current is passed through DNA fragments move towards positive anode (negative charge on phosphate groups) Fragments move at varied rates dependent on mass/charge Once electrophoresis is complete UV light is shone to display DNA Southern blotting alkaline buffer added nylon filter paper placed over gel dry absorbent paper used to draw solution containing DNA fragments to filter leaving them as blots on the filter Alkaline solution denatures DNA fragments strands separate base sequences observable Experiment: Polymerase chain reaction Mix DNA sample, primers (small sequences of DNA which must join to the beginning of the separated DNA strands before copying can begin) and many of the four nucleotide bases into a PCR machine Mixture is heated to 90oC breaking hydrogen bonds and DNA strands Mixture cooled to 55oC so primers bind to single DNA strands Heated to 75oC optimum temperature for DNA polymerase to build complementary strands of DNA DNA profiling and identification of genetic relationships between organisms 1) 90% of DNA is made of introns - regions of chromosomes used for DNA profiling 2) Within introns there are short sequences of DNA repeated many times forming microsatellites (2-4 bases repeated 5-15 times) and mini-satellites (20-50 repeated 50-100 times). 3) The same micro/mini-satellites appear in the same positions on each pair of homologous chromosomes 4) Number of repeats of each satellite vary as different patterns are inherited from mother/father 5) Many different introns with a huge variation in the number of repeats likelihood of two individuals having same pattern of DNA is low. 6) More closely related individuals are more likely it is that similarities will be apparent in DNA patterns. Inflammation 1)Mast cells and damaged white blood cells release histamines 2)Histamines cause blood vessels to dilate, increasing blood flow 3)Raised temperature reduces effectiveness of pathogen reproduction 4)The walls of the capillaries also leak as the cells forming the walls separate slightly (increase in permeability) 5)Fluid including plasma, white blood cells and antibodies are forced out of the capillaries causing swelling and pain.

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The humoral response Pathogen enters body Macrophage engulfs pathogen vesicle containing pathogen fuses with lysosome Enzymes in lysosome break down pathogen separates off the antigens Inside macrophage antigens combine with MHC These complexes move to surface of cell outer membrane Macrophage + antigen/MHS on cell surface = antigen-presenting cell CD4 receptors on the outer membrane of the T helper cell enable it to bind to specific antigen of the antigen/MHC complex T helper cell reproduce clone of the cells New cells have same CD4 receptors as original T helper cell specific for original antigen Cloned cells become active T helper cells Some clone cells become T memory cells remain in the body to become active if same antigen is encountered again. Effector stage: T helper cells and B cells active Different B cells which have immunoglobulins specific for antigen are presented by the pathogen they bind to it B cell then engulfs pathogen by endocytosis Vesicle formed fuses with a lysosome Enzymes break down antigen leaving fragments of processed antigen These become attached to MHC another APC forms T helper cell from active clone recognises antigen displayed on MHC complex on B cell Cytokines released from T helper cell stimulate B cell to divide and form a clone of identical cells. B effector cells and B memory cells Cloning of b cells eventually forms correct antibodies clonal selection B effector cells differentiate into plasma cell clones which produce antibodies (species protein released into circulation- identical to immunoglobulin of original parent B cell) Antibodies bind to specific antigens on pathogens which cause their destruction Microorganisms agglutinate/clump together preventing their spread Antigen-antibody complex readily engulfed and digested by phagocytes Stimulate other reactions within body destruction of membrane release of histamine by invaded cells causing inflammation B memory cells produced by divisions of B cell APC Allow body to respond rapidly to second invasion by same antigen Cell-mediated response Pathogen digested surface antigens become bound to MHC forming APC T killer cells present in blood complementary receptor proteins Bind to antigen/MHC surface of body cell T killer cells exposed to cytokines active T helper cell cell divisions clone of identical T killer cells bind to infected body cells T killer cells release enzymes pores appear in membrane of infected cells Free entry of water and ions cells swell and burst Any pathogens intact are labelled with antibodies produced by B effector cells destroyed

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TB Bacteria inhaled into lungs multiply slowly for primary infection Localised inflammatory response tubercule forms with dead bacteria and macrophages 8 weeks immune system controls the bacteria inflammation dies down lung tissue heals. If it avoids the immune system it may survive primary infection stage Bacteria thick waxy outer layer protects them from enzymes of macrophages Bacteria remains in tubercules dormantly growing - effective bacteria selected/ passed on When immune system is not working well active tuberculosis is produced, Bacteria multiply rapidly in lungs Symptoms of TB fever, night sweats, loss of appetite, loss of weight. Infection in lungs cough lung tissue damaged cough up blood T cells targeted reduced production of antibodies TB run a temperature denaturing enzymes Insufficient oxygen/ organs fail due to lack of nutrition HIV causes AIDS 1)HIV attaches to CD4 receptors on T helper cells and infects them 2)Takes over host DNA and replicates 3) Viruses leave T helper cell and destroy it 4) Host T killer cells destroy heavily infected T helper cells reducing their number 5) Activation of macrophages and T killer cells doesnt occur Normal functioning of T helper cells is lost immune system cant fight off other pathogens HIV/AIDS infection Stage 1 acute HIV syndrome Fevers, headaches, tiredness, swollen glands 3-12 weeks after infection HIV antibodies appear in blood HIV positive Stage 2 asymptomatic /chronic - Infection established symptoms disappear Virus replicates infecting CD4 T helper cells Secondary infections develop immune system overwhelmed Stage 3 symptomatic disease immune system fails T helper cell count falls Patients suffer HIV related symptoms Weight loss, fatigue, diarrhoea, night sweats, thrush Stage 4 advanced aids T helper cell fall Weight loss / dementia/ cancers/ TB Experiment: Effects of antibiotics 1) Place some bacteria on an agar plate 2) Place discs of absorbent filter paper in different antibiotics / different concentrations of the same antibiotic 3) Have one disc of absorbent paper in only ethanol (control) 4) Place the paper discs on the agar plate with the bacteria on it same conditions and same time 5) Incubate the plate (cover it) to allow the bacteria to grow 6) Where the bacteria is prevented from growing there will be a clear area called the inhibition zone 7) The larger the inhibition zone the more effective the antibacterial properties of the antibiotic

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Glossary Stroma matrix in chloroplast containing enzymes Thylakoid chlorophyll molecules are found Grana stacks of thylakoid Photolysis decomposition of water to H+, e- and O2 Photophosphorylation the production of ATP using energy from sunlight NPP = GPP - R Biotic factors (living factors)- predation, mate-finding, territory, parasitism and disease, competition Abiotic factors (non-living factors) - light, temperature, wind and water current, water availability, oxygen availability, soil structure Carbon sink carbon is removed from the atmosphere and stored biotic: photosynthesis / abiotic stored in rocks Speciation the formation of two new species from one species Reproductive isolation the separation of one species into two populations that dont interbreed Pre-zygotic isolation fertilisation is prevented Habitat isolation populations go into different habitats so they dont come in contact during reproductive season Temporal isolation populations out of reproductive time synchronisation Mechanical isolation mutation resulting in physical barrier to isolation Behavioural isolation may not recognise others as mating partners Post-zygotic isolation failure to breed Low hybrid zygote vigour zygote (sperm fertilised egg) fails to develop properly Low hybrid adult viability offspring fail to thrive/ grow Hybrid infertility offspring may appear healthy but are infertile Antisense strand RNA strand as template of DNA Allele frequency the relative proportion of different forms of a particular gene within a gene pool Triplet code sequence of three bases forming a codon Virus structure capsid, capsomere, nucleic acid Bacterial structure mitochondria, nucleic acid, mesosome, plasmid

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Pathogen invading microorganisms Antigen substance that stimulates the production of an antibody Antibody immunoglobulins fight antigens Bacteriocidal antibiotics kills bacteria Bacteriostatic antibiotics prevents bacteria from multiplying Vaccination procedure through which people are immunised Natural active immunity immune system of the body Natural passive immunity antibodies from mother to baby providing it with temporary immunity until its bodys immune system becomes activated. Artificial passive immunity antibodies formed in one individual extracted and injected into another. Artificial active immunity some amounts of a weakened antigen are used to produce immunity immune system produces antibodies against the antigen and memory cells form so if real pathogen enters body it is prepared to destroy it immediately. Independent/ dependent variables in an experiment e.g. where the effect of varying temperatures on enzyme activity is measured, the independent variable would be the temperature and the dependent variable would be enzyme activity. Extraneous variable anything other than what is being changed that may affect the outcome of the experiment e.g. if effect of changing light on plant growth was being measured, volume of water available may be an extraneous variable.

Adam Clarke www.brain-freeze.co.uk