Biology

1. Biology xX...TheDitzyBlonde...Xx

2. Contents • Respiration • Photosynthesis • Microbiology • Populations • Homeostasis • Nervous system

3. Respiration

4. Need for ATP • Movement • Homeostasis • Anabolic processes (synthesis of large molecules from smaller ones) • Active transport • Secretions

5. ATP • Temporary energy store • Must be used in cell where it is created • Base = adenine • Pentose sugar = ribose • 3 phosphate groups • Adenosine triphosphate • Hydrolysis of ATP is exergonic (energy released)  catalysed by ATPase • Phosphorylation of ADP endergonic (energy used) • 30 kJ mol-1 energy to add/remove phosphate group  catalysed by ATPsynthetase

6. Cellular respiration • Gas exchange = diffusion of gases into and out of cells that allows respiration to take place • Respiration = series of oxidation reactions that take place in living cells resulting in the release of energy from organic respiratory substrates e.g glucose • Aerobic or anaerobic • Obligate anaerobes = only carry out anaerobic respiration because they are poisoned by the presence of oxygen

7. Glycolysis • In cytoplasm of cells • Glucose (6C) phosphorylated to glucose phosphate (6C)  ATP hydrolysed to ADP • Glucose phosphate (6C) phosphorylated to fructose bisphosphate (6C)  ATP hydrolysed to ADP • Fructose bisphosphate (6C) unstable so breaks down to form 2x glycerate-3-phosphate (3C) • 2x glycerate-3-phosphate (3C) converted to pyruvate (3C)  4 ADP phosphorylated to 4 ATP, 2 NAD reduced to 2 NADH • Net gain of 2 reduced NAD and 2 ATP

8. Link reaction • In mitochondria • 2x pyruvate (3C) from glycolysisdecarboxylated and dehydrogenated to form 2x acetate (2C)  carbon dioxide and reduced NAD formed • 2x acetate (2C) combines with 2x coenzyme A to form 2x acetyl coA • Net gain of 2 carbon dioxide molecules and 2 molecules of reduced NAD

9. Krebs cycle • In matrix of mitochondria • Acetyl coA (2C) from link reaction combines oxaloacetate (4C) to form citrate (6C) • Citrate (6C) decarboxylated and dehydrogenated to regenerate oxaloacetate (4C)  reduced NAD, reduced FAD, ATP and carbon dioxide formed • Net gain of 6x reduced NAD, 2x reduced FAD, 2x ATP and 4x carbon dioxide per molecule of glucose

10. Electron transport chain • Inner membrane of mitochondria • Hydrogen atoms from NAD and FAD passed down chain of carrier molecules • Hydrogen atoms split into hydrogen ions and electrons • Electrons transferred along electron carriers  each at lower energy level than previous so energy is released, which is used to make ATP (oxidative phosphorylation) • Hydrogen ions stay in solution in inner membrane space of mitochondria • Oxygen is the final electron acceptor of the electron carrier chain  electrons, hydrogen ions and oxygen combine to form water, catalysed by cytochromeoxidase • 3x ATP made per reduced NAD, 2x ATP made per reduced FAD • 34x ATP made per glucose molecule (+ 2 from glycolysis and 2 from Krebs cycle, so overall gain of ATP per glucose molecule for aerobic respiration is 38x ATP)

11. Chemiosmotic theory • Mitochondria have a double membrane • Inner membrane folded to form cristae large surface area • Cristae lines with stalked particles that contain ATPsynthetase enzymes • Energy released by electron transport chain pumps hydrogen ions from matrix to inner membrane space • Higher concentration of hydrogen ions in inner membrane space than in matrix sets up an electrochemical gradient • Hydrogen ions diffuse back into matrix through stalked particles, down electrochemical gradient • Electrical potential energy of diffusion of hydrogen ions used to make ATP, using ATPsynthetase as a catalyst

12. Anaerobic respiration • Fermentation = anaerobic respiration of yeast, 2% efficiency approx  pyruvate converted to ethanal and carbon dioxide, hydrogen from reduced NAD used to turn ethanal to ethanol • Ethanol toxic if accumulated by yeast • Lactate formed when muscles carry out anaerobic respiration, 2% efficiency approx  pyruvate reduced to form lactate • Lactate transported to liver via bloodstream  1/5 approx converted back to pyruvate and used in aerobic respiration, 4/5 converted to glycogen • Oxygen debt = oxygen required to break down lactate

13. Other respiratory substrates • Lipids  fats hydrolysed to fatty acids and glycerol  fatty acids broken down in matrix to acetyl fragments (2C)  these combine with coA to form acetyl coA  enters Krebs cycle  glycerol phosphorylated to glyceraldehyde-3-phosphate, enters glycolysis • Protein  hydrolysed to amino acids  these deaminated in liver  organic acid produced fed into Krebs cycle

14. Photosynthesis

15. Photosynthesis • Carried out by photoautotrophs • Takes place in chloroplasts found in the mesophyll cells and guard cells of green leaves • Sunlight trapped by the photosynthetic pigments e.g. chlorophyll • Light, carbon dioxide, water and a suitable temperature  is needed for photosynthesis to occur • Carbon dioxide + water (+ light energy)  glucose + oxygen • 6CO2 + 6H2O (+ light energy) C6H12O6 + 6O2 • Endergonic  reaction which occurs in two stages catalysed by enzymes; the light-dependent stage and the light-independent stage

16. Factors affecting photosynthesis • Limiting factors are conditions that prevent the rate of photosynthesis increasing • For photosynthesis, limiting factors can be light intensity , temperature , carbon dioxide concentration , and volume of water  available • Compensation point  is when carbon dioxide produced by respiration is completely reused during photosynthesis • Rate of photosynthesis can be found by measuring either the rate carbon dioxide is used or the rate glucose is produced or the rate oxygen is produced • Photosynthometers calculate the rate of photosynthesis by measuring the volume of oxygen produced in a period of time

17. Leaf structure and function • Large surface area to absorb as much sunlight as possible • Thin so light can penetrate them, and giving a short diffusion path for carbon dioxide • Cuticle  and epidermis  are transparent so light can pass through them • Palisade mesophyll cells contain lots of chloroplasts and have their long axes parallel to the surface • Chloroplasts can move intracellularly by cyclosis  so they can arrange themselves for the most efficient absorption of light • Chloroplasts hold chlorophyll in an ordered arrangement • Stomata allow carbon dioxide to enter the leaf

18. Photosynthetic pigments • Absorb light energy and convert it to chemical energy • Found in the thylakoid membranes  of the chloroplast in groups called antenna complexes  • Photons of light energy are passed along antenna complex until they reach a chlorophyll a molecule at the reaction centre of a photosystem • Chlorophylls absorb mainly red and blue-violet frequencies of light  • Chlorophyll molecules have a hydrophilic  head containing a magnesium ion  and a hydrophobic  tail • Chlorophyll a and chlorophyll b are the most common types of chlorophyll • Chlorosis is a condition where plants are magnesium deficient so cannot produce enough chlorophyll and look yellow in colour • Carotenoids  are accessory pigments  that absorb mainly blue-violet frequencies of light • Carotenes and xanthophylls are the two main types of carotenoids • Having a range of different photosynthetic pigments allows more energy to be harnessed for photosynthesis as different pigments have different absorption spectra • Plants look green because very little green light is absorbed  by the photosynthetic pigments

19. Absorption and action spectra • Wavelengths of light are either absorbed or reflected by pigments • The absorption spectrum indicates which wavelengths of light are absorbed by pigments • The action spectrum shows the amount of carbohydrates synthesized (rate of photosynthesis) at different wavelengths of light • The action and absorption spectrums for chlorophyll are closely correlated, providing evidence that chlorophyll is a pigment responsible for absorbing light for photosynthesis

20. Chromatography • Separated using chromatography  • Pigments are extracted by grinding a leaf using a pestle and mortar, and a solvent such as propanone • Origin line  is drawn a couple of centimetres from the bottom of the chromatography paper, and an extract of the ground leaf is added on the origin line • The chromatogram is placed in a glass tank containing a solvent, with the level of the solvent just below the origin line, and left to allow the solvent to rise up through the chromatography paper • Pigments rise up the chromatography paper different distances depending on the relative solubility in the solvent • When the solvent front reaches the top of the chromatography paper, the paper is taken out and dried • Rf value  calculated and used to identify the pigment • Rf value = distance travelled by pigment/distance travelled by solvent front

21. Harvesting Light • Accessory pigments (chlorophyll b and carotenoids) and primary pigment (chlorophyll a) found in thylakoid membranes of chloroplasts in group/clusters called antenna complexes • Photons of light passed from accessory pigments to the primary pigment (chlorophyll a) in a reaction centre • Two types of reaction centre, photosystems 1 and 2

22. Light Dependent Stage • Takes place in thylakoids of chloroplasts • ADP and Pi synthesised to ATP by photophosphorylation • Water is split into 2H+, 2e-’s and ½ O2 by photolysis • NADP is reduced by 2H+’s from photolysis of water • Two forms of LDS  cyclic photophosphorylation and non-cyclic photophosphorylation

23. Non-Cyclic Photophosphorylation • Also known as Z-scheme • Light absorbed by PSII and passed on to chlorophyll a (P680) • Chlorophyll a emits 2 e-’s, which are raised to a higher energy level and picked up by an electron acceptor • Electron’s passed along a chain of carrier molecules until it is eventually accepted by PSI • Energy released when electrons are passed down chain of carrier molecules is used for photophosphorylation of ADP and Pi to ATP • Light absorbed by PSI and passed onto chlorophyll a (P700), which emits 2 e-’s • Electrons raised to higher energy level and picked up by an electron acceptor • Electrons passed down (shorter) carrier molecule chain until accepted by NADP • Photolysis of water produces 2H+, which combines with NADP to give reduced NADP, 2e-’s which replace electrons lost from PSII and ½ O2 which is emitted as a waste product • Reduced NADP and ATP passed onto light independent stage

24. Cyclic Photophosphorylation • Only involves PSI • Light absorbed by PSI and passed onto chlorophyll a (P700) • Chlorophyll a molecule emits an electron • Electron is raised to a higher energy level and is picked up by an electron acceptor • Electron passed along a carrier molecule chain until it recombines with PSI • Energy emitted when electrons are passed along carrier molecule chain used for photophosphorylation of ADP and Pi to ATP • No reduced NADP is made • ATP is passed onto the light independent stage

25. Chemiosmosis • ATP is synthesised form ADP and Pi by enzyme ATP synthetase found in the thylakoid membranes • Energy emitted as electrons are passed down the carrier molecule chain in light dependent stage used to pump hydrogen ions from stroma to the thylakoid membrane space, creating an electrochemical gradient across the thylakoid membrane • Hydrogen ions diffuse down the electrochemical gradient through the thylakoid membrane via protein channels • Shape of ATP synthetase changed so that ATP can be synthesised from ADP and Pi

26. Light Independent Stage • Also known as Calvin Cycle • Carbon dioxide combines with ribulose bisphosphate (RuBP) using enzyme RuBP carboxylase as a catalyst • Product of unstable 6C compound formed, which decomposes into 2x 3C molecules of glycerate 3-phosphate (GP) • ATP used to phosphorylate 2x 3C molecules of GP to 2x 3C molecules of glycerate bisphosphate • Reduced NADP acts as reducing agent to reduce glycerate bisphosphate to glyceraldehyde 3-phosphate (GALP) • 1/6 of GALP produced is converted to glucose and other respiratory substrates • 5/6 of GALP produced is used in a series of enzyme catalysed reactions to regenerate RuBP

27. Microbiology

28. White blood cells • Also known as leucocytes • Defend body against pathogens • Pathogens are disease causing organisms • Made in bone marrow by division of stem cells • Neutrophils are lobed and largest of leucocytes  role is phagocytosis • Lymphocytes are small with a large, round nucleus • B-lymphocytes produce antibodies (humoral response) • T-lymphocytes are involved with the cell-mediated response • Monocytes are large with a kidney shaped nucleus  develop into macrophages • Eosinophils are associated with allergies • Basophils release chemicals such as histamines that cause inflamation

29. Types of bacteria • Coccus spherical • Spirillum spiral shape • Bacillus  rod shaped • Gram positive  retains crystal violet dye because crystal violet is trapped in the peptidoglycan wall • Gram negative  retains saffronin because lipopolysaccharide layer that prevents crystal violet being trapped in the peptidoglycan wall is made more permeable by the crystal violet dye, so that the counter stain saffronin can be taken up by the peptidoglycan wall

30. Bacterial growth • Lag phase is when the pathogen is active but there is little growth as they are taking up water and producing enzymes • Exponential/log phase is where the population size increases rapidly • Carrying capacity is when the maximum population the environment can support is reached • Stationary phase is when the pathogens are dying at the same rate as they are produced • Death phase is when pathogens are dying faster than they are being produced due to lack of nutrients, lack of oxygen or accumulation of toxic waste products

31. Factors affecting growth • Temperature • Thermophiles have optimum temperature of above 40 degrees  grow in hot springs, compost heaps and water heaters • Mesophiles have optimum temperature between 20 and 40 degrees  most bacteria including human pathogens • Cryophiles have optimum temperature below 20 degrees  live in Arctic and Antarctic Oceans, fridges and freezers • pH • Most have optimum of pH 7 and cannot function below pH 4 • Bacteria produce waste products with low pH and can lead to death of bacteria population • Oxygen • Needed for aerobic bacteria to produce ATP • Obligate anaerobes are killed if oxygen is present • Nutrients • Essential for growth • Nitrogen needed for protein synthesis

32. Culturing bacteria  aseptic technique • Cuts covered with clean, waterproof dressing • No food or drink in lab • Windows and doors closed to avoid airborne contamination • Wash hands with anti-bacterial soap before and after • Wipe down bench with disinfectant before and after • Tape petri dish securely after inoculation and label them • Keep temperature below 30 degrees • Sterilise all containers using autoclave (121 degrees for 15 mins) before and after to destroy spores • Sterilise equipment throughout innoculation by placing in alcohol then burning off alcohol with bunsen flame • Work near lit bunsen burner to produce convection currents to kill airborne infections • Lift petri dish lid at 45 degree angle • Do not open petri dishes after inoculation

33. Culturing bacteria • Wash hands and disinfect bench • Label petri dish • Dip inoculating loop in alcohol and burn off using bunsen flame • Unscrew bottle of microbe sample and hold opening in bunsen flame for 2 seconds • Dip sterile inoculation loop into microbe sample and replace lid of bottle • Lift lid of petri dish slightly and streak inoculating loop over surface of the agar • Replace lid and seal with tape • Put dish upside down in incubator at 25 degrees for 2-3 days • Wash hands and disinfect bench

34. Monitoring growth • Haemocytometers are modified microscope slides divided into squares • A type squares have side length 1mm • B type squares have area of 0.04 square mm  25 B squares per A square • C squares have area 0.0025 square mm  16 C squares per B square • Number of cells in a particular type of square countedusing a microscope • Used to calculate number of cells per cubic mm

35. Disadvantages of haemocytometer method of monitoring growth • Unreliable due to small volume of sample used • Can’t differentiate between viable (living and able to reproduce) and dead cells so can get inaccurate totals • Debris in sample may obscure cells to be counted

36. Dilution plating • Culture medium diluted • Small sample of each dilution placed on agar plate • Plates incubated between 25 and 30 degrees for 2-5 days • Plates examined and colonies counted • Assumption that each colony comes from a single cell • Total viable cell count = number of colonies x dilution factor

37. Turbidimetry • Colorimeter used to measure turbidity (cloudiness) • Amount of light absorbed measured • More cells = more light blocked • Results compared to calibration curve  graph of absorbance of known concentrations of cells • Assumes turbidity caused solely by microorganisms • Mixture must be continually stirred to prevent settling

38. Populations

39. Carbon cycle • Carbon used for photosynthesis, dissolves from atmosphere into seawater • Released back into environment by respiration, respiration of decomposers, combustion of fossil fuels

40. Nitrogen cycle • Nitrogen is an unreactive gas  converted to nitrates so it can be used by plants and transferred along food chain • Ammonification is the breakdown of proteins, amino acids and urea by decomposing bacteria to form nitrogen • Nitrification is the conversion of ammonium ions to nitrates under aerobic conditions by nitrofying bacteria  nitrosomonas oxidises ammonium ions to nitrites, nitrobacter oxidises nitrites to nitrates, which can enter the food chain • Nitrogen fixation is the conversion of nitrogen in the atmosphere to nitrates by nitroge-fixing bacteria  azotobacter in the soil, nostoc in freshwater, rhizobium found in root nodules of legume plants • Denitrification is the conversion of nitrates and ammonium ions back to nitrogen gas by denitrifying bacteria in the absence of oxygen  pseudomonas and thiobacillus in water-logged soils carry out denitrification to gain their energy

41. Populations • Group of individuals of same species living in same place at same time and interbreeding • Population growth causes competition for resources and space • Better adapted individuals of the population are more likely to survive and reproduce, passing on their genes to their offspring • Adaptations may make the individual more successful in breeding and rearing their young, better at protecting themselves and offspring from predators, better at locating food sources etc

42. Determining population growth • Birth rate = reproductive capacity of population • Mortality = death rate of organisms in the population • Immigration = movement of individuals into the population • Emigration = movement of individuals out of a population

43. Population growth • Exponential growth when conditions are favourable • Boom and bust curve caused by exponential growth followed by rapid decrease in population caused by a limiting factor • Biotic potential = maximum rate of reproduction when their are no other limiting factors • Environmental resistance = factors that limit growth of population e.g accumulation of waste products, lack of resources, climatic conditions, predators, parasites, competitors • Carrying capacity = maximum population size that can be supported by a particular environment • S-shaped curve = lag phase, log phase, stationary phasem decline phase (see microbiology)  occurs when species colonise new habitats

44. Environmental resistance • Abiotic factors = climate, oxygen levels, water quality, pollution • Biotic factors = competition for resources/space, parasites, predators • Density-independent factors affect all plants and animals of the population, regardless of population size  climate, pollution, disease • Density-dependent factors vary in effect on population depending on population size  competition for resources, predation, parasites (always biotic, never abiotic)

45. Competition • Intraspecific competition = competition between organisms of the same species caused by over-reproduction  density-dependent • Interspecific competition = competition between organisms of different species • Competitive exclusion principle says interspecific competition is most intense when two different species occupy the same niche

46. Predation • Good predators have means to kill, speed to pursue prey and camouflage for stalking prey • Group hunting allows prey to be surrounded • Young, old or sick prey targeted as easier to kill • Large prey gives more food per kill • Variety of prey species reduces chance of starvation • Migration to areas with plenty of prey species reduces chance of starvation • Prey adapt to be faster than predator, stay in large groups, have stings, taste bad and have warning coloration, are camouflaged in the environment, have startle mechanisms to confuse predator

47. Predator-prey cycles • Fluctuations in predator numbers smaller than fluctuations in prey numbers • Fluctuations in predator numbers lag behind fluctuations in prey numbers • Fewer predators than prey

48. Biological control • Use of predators, parasites and pathogens to keep pests levels below the economic damage threshold • Economic damage threshold = pests causing enough damage that it is worth spending money to control the pest • Biological control agent = predator, parasite or pathogen used must be specific to the pest, high initial expense, inexpensive once established, slow to react, crops may suffer from several pests so more than one biological control may be required, biological control agent may need to be reintroduced if crop is only sometimes affected by the pest

49. Homeostasis

50. Homeostasis • Maintenance of a constant internal environment • Receptors detect a stimulus • Stimulus is a change in the level of the factor being regulated • Input is a detectable change • Coordinator receives info from receptor and triggers action to correct the change • Effector brings about a change  corrective mechanism