Aqa a2 biology unit 4 complete

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Aqa a2 biology unit 4 complete

  1. 1. AQA A2 Biology Unit 4 Populations
  2. 2. Specification 3.4.1 The dynamic equilibrium of populations is affected by a number of factors. Candidates should be able to: • carry out experimental and investigative activities, including appropriate risk management • consider ethical issues when carrying out fieldwork, chiefly those relating to the organisms involved and their environment • analyse and interpret data relating to the distribution of organisms, recognising correlations and causal relationships • appreciate the tentative nature of conclusions that may be drawn from such data. • interpret growth curves, survival curves and age-population pyramids • calculate population growth rates from data on birth rate and death rate. • relate changes in the size and structure of human populations to different stages in demographic transition. Populations and Variation in population Investigating populations Human populations ecosystems size A population is all the organisms of one species in a habitat. Populations of different species form a community. Within a habitat a species occupies a niche governed by adaptation to both biotic and abiotic conditions. A critical appreciation of some of the ways in which the numbers and distribution of organisms may be investigated. Random sampling with quadrats and counting along transects to obtain quantitative data. The use of percentage cover and frequency as measures of abundance. The use of mark– release–recapture for more mobile species. Population size may vary as a result of • the effect of abiotic factors • interactions between organisms: interspecific and intraspecific competition and predation. Population size and structure, population growth rate, agepopulation pyramids, survival rates and life expectancy.
  3. 3. Definitions • Abiotic: Ecological factor that makes up part of the non-biological environment • Biotic: Ecological factor that makes up part of the living environment • Ecosystem: More or less self contained functional unit in ecology made up of all interacting biotic and abiotic factors in a specific area • Population: A group of individuals of the same species that occupy the same habitat at the same time • Species: A group of similar organisms that can breed together to produce fertile offspring • Community: The organisms of all species that live in the same area • Habitat: The place where an organism normally lives, which is characterised by physical conditions and the species of other organisms present • Niche: All conditions and resources required for an organism to survive, reproduce and maintain viable population • Intraspecific: Competition between organisms of the same species • Interspecific: Competition between organisms of different species • Predator: An organism which feeds of another organism known as the prey
  4. 4. 1.1 Populations and Ecosystems The environment can include abiotic and biotic factors such as temperature, light (abiotic), predation and competition (biotic) The life supporting layer of land, air and water that surrounds the earth is known as the biosphere Ecosystems • The ecosystem is made up of biotic and abiotic features • There are two major processes to consider: • The flow of energy through the system • The cycling of elements within the system • There are a number of species in an ecosystem which make up many groups of individuals that together make up a population
  5. 5. 1.2 Investigating Populations When studying a habitat the number of individuals in an individual space needs to be counted this is the abundance Only small samples are taken due to the time consuming nature As long as samples are representative the conclusions will be valid Factors to consider when using quadrates: • Size of quadrat: Larger species need larger quadrats, if a species occurs in series of groups then a large number of small quadrats is used • Number of samples: The larger the number the more reliable the results • Position of quadrat: Statistically significant results are obtained by random sampling Random Sampling • To avoid bias random sampling is used • 1. Lay out two long tape measures at right angles along two sides of the study area • 2. Obtain series of coordinates by using random numbers taken from a computer • 3. Place a quadrat at the intersection of each pair of coordinates and record the species within it Systematic sampling along Transects • A line transect can be used in which a string/tape is stretched across the ground and any organism that passes the line is recorded • A belt transect is a strip marked using a second parallel line, species within the belt and between the lines are recorded
  6. 6. Measuring Abundance • Random sampling and counting along transects can obtain measures of abundance in several ways: • Frequency: Likelihood of a particular species occurring in a quadrat. It gives quick idea of species present and general distribution within an area but doesn’t provide density or distribution of species • Percentage Cover: Estimate of the area within a quadrat. Useful where species is particularly abundant, data can be collected rapidly bur it occurs in overlapping layers • To obtain reliable results the sample size needs to be large and a mean needs to be collected Mark-releaserecapture • Due to animals being mobile this method is used • Once an animal is caught it is marked then released, later on more individuals are captured and the number marked is recorded • The technique relies on assumptions: • Proportion of marked to unmarked individuals in the second sample is the same as the proportion of marked to unmarked individuals in the population as a whole • The marked individuals released from the first sample distribute themselves in sufficient time • The population has a definite boundary so no immigration or emigration • There are few deaths and births • The marking is not toxic or makes the animal more liable to predation • The mark or label is not lost or rubbed off Analysing data • The first stage is to present data in a table or graph so data can be compared and then calculate standard deviation • Correlation and causation can be analysed • Statistical tests can also be used to calculate strength and direction of any correlation • Spearman rank, chi squared and standard error can be used
  7. 7. Population = Total number of individuals in the first sample X Individuals in the second sample Number of marked individuals recaptured Type of Trap Method of Marking Pitfall trap: Insects, Small Mammals Microchip Electrofishing : Fish Paint or permanent marker onto animal Cage set up with food in: Mice, Voles Photo showing unique markings Removal method: blocks of part of environment so can collect fish Visible implant or tag Glue Trap: Rodents Toe Clippings: Vertebrates Sweepnet moved through plants: Ground insects Fur Removal Wire funnel trap: Insects in tall vegetation
  8. 8. 1.3 Variation in Population Size Population Growth Curves • 1. Period of slow growth as the initially small number of individuals reproduce to slowly build up their numbers • 2. Period of rapid growth where the ever increasing number of individuals continue to reproduce. The population size doubles during each interval • 3. Period when population growth declines until size becomes stable, the decline can be due to food shortage or predation There are 3 phases: 2. 1. 3.
  9. 9. Population Size Population size depends on limiting factors: Abiotic Factors • • • • • Mineral ions Light Temperature Oxygen Food • Temperature: Optimum temperature needed for best survival as otherwise enzymes work slower and metabolic rate is reduced due to denaturation • Light: Ultimate source of energy, the stronger the light intensity the faster the rate of photosynthesis causing a faster growth of plants thus a larger population • pH: Optimum pH needed otherwise enzymes don’t work to full potential as denatured • Water/Humidity: In low water areas only species well adapted to dry conditions survive. The more humid an area the slower the rate of transpiration
  10. 10. 1.4 Competition Intraspecific Competition Interspecific Competition • Between the same species • Compete for food, water, mates • Greater the resources availability the larger the population • Between different species • For food, light and water • If two species occupy in the same niche one will normally have a competitive advantage • The population of the stronger species will gradually increase while the other diminishes eventually to be removed: Competitive exclusion principle • No species can occupy the same niche indefinitely when resources are limiting
  11. 11. Intraspecific Competition Interspecific Competition
  12. 12. 1.5 Predation The relationship between prey and predator: • Predators eat their prey, reducing prey population • The predators become in greater competition with each other over the prey left • Predator population is reduced causing fewer prey to be eaten • The prey population increases • Due to more prey the predator population then increases The fluctuations in population as also due to disease and climatic factors not just predation Population crashes create selection pressure where survival of the fittest occurs, the survivors will reproduce • The population then evolves to be better adapted to harsh conditions
  13. 13. 1.6 Human Populations There has been an explosion in human population due to: • The development of agriculture • The development of manufacturing and trade that created industrial revolution War, disease and famine have only been temporary reversals in the upward trend Factors affecting Growth • Birth rate • Death rate • Immigration: Individuals join a new population • Emigration: Individuals leave a population Population Growth = (Births + Immigration) – (Deaths + Emigration) Percentage Population Growth Rate: Population change during the period Population at the start of the period X 100
  14. 14. Birth Rate Factors Death Rate Factors Birth Rate: number of births per year Total population in the same year X1000 Death Rate: number of deaths per year Total population in the same year X1000 • Economic conditions: Lower capita income tend to have higher birth rates • Cultural/Religious: Some religions oppose birth control • Social pressure: Large families can improve social standing • Birth Control: Contraception isn't always available • Political factors: Government influence births via education and taxation • Age Profile: The more elderly people the higher the death rate • Life expectancy: ECDLs have lower life expectancies • Food supply: Need a balanced diet • Sanitation: Reduces water-borne deaths e.g. cholera • Medical care availability • Natural disasters: Higher death rates near droughts • War
  15. 15. Population Structure • Well economically developed countries have a higher life expectancy, this has led to change in societies from short life expectancies to long life expectancies causing demographic transition Stable Population Population pyramids can be used to plot populations: Survival Rates • Stable Population: Birth and death rate are balanced so no decrease or increase in population • Increasing Population: High birth rate (shows wider base) and fewer old people (narrow apex) • Decreasing Population: Lower birth rate (narrow base) and low mortality rate so more elderly people (wider apex) Increasing Population • Plotting as survival curve allows life expectancy to be calculated Decreasing Population
  16. 16. AQA A2 Biology Unit 4 ATP & Photosynthesis
  17. 17. Specification 3.4.2 ATP provides the immediate source of energy for biological processes. 3.4.3 In photosynthesis, energy is transferred to ATP in the light-dependent reaction and the ATP is utilised in the light-independent reaction. Candidates should be able to explain how growers apply a knowledge of limiting factors in enhancing temperature, carbon dioxide concentration and light intensity in commercial glasshouses. They should also be able to evaluate such applications using appropriate data. ATP The synthesis of ATP from ADP and phosphate its role as the immediate source of energy for biological processes. Photosynthesis The lightindependent and lightdependent reactions in a typical C3 plant. Light-dependent reaction • light energy excites electrons in chlorophyll • energy from these excited electrons generates ATP and reduced NADP • the production of ATP involves electron transfer associated with the electron transfer chain in chloroplast membranes • photolysis of water produces protons, electrons and oxygen. Light-independent reaction • carbon dioxide is accepted by ribulose bisphosphate (RuBP) to form two molecules of glycerate 3-phosphate (GP) • ATP and reduced NADP are required for the reduction of GP to triose phosphate • RuBP is regenerated in the Calvin cycle • Triose phosphate is converted to useful organic substances. Limiting factors The principle of limiting factors as applied to the effects of temperature, ca rbon dioxide concentration and light intensity on the rate of photosynthesis.
  18. 18. Definitions • • • • • • • • • • ATP: An activated nucleotide found in all living cells that acts as an energy carrier Endothermic: Reaction that requires energy Activation Energy: Minimum energy required to bring about a chemical reaction Hydrolysis: The breaking of large molecules to small using water Condensation: Chemical process where two molecules form a larger molecule Electron carrier molecules: A chain of carrier molecules along which electrons pass, releasing energy in the form of ATP Thylakoids: Series of flattened membranous sacs in a chloroplast that contain chlorophyll and the associated molecules needed for the light-dependent reaction NADP: Molecule that carries electrons produced in the light-dependent reaction Stomata: Pores surrounded by guard cells that allow gas diffusion Stroma: Matrix of chloroplast where the light-independent reaction occurs
  19. 19. 2.1 Energy and ATP All living organisms require energy to stay alive Plants use solar energy from the sun to combine water and CO₂ in photosynthesis The organic molecules formed are broken down by plants and animals into ATP Energy Why Energy is Needed • Energy can take many forms such as light and kinetic • Energy cannot be created or destroyed • It is measured in joules(J) • It can change from one form to another • Metabolism: All reactions in the body require energy • Movement: For in and out of the body itself • Active Transport: Ions and molecules need to be transported against the concentration gradient across plasma membranes • Repair and Division • Production of Substances: Such as enzymes and hormones • Maintenance of body temperature: Mammals and birds are endothermic and need energy to replace that lost to the environment
  20. 20. Energy and Metabolism • 1. Light energy from the sun is converted by plants into chemical energy during photosynthesis • 2. The chemical energy from photosynthesis, organic molecules, is converted into ATP during respiration • 3. ATP Is used by cells Storing ATP • ATP has 3 phosphate groups which have unstable bonds thus a low activation energy so are easily broken • Energy is released when the bonds break • The reaction uses water to is a hydrolysis reaction • ATP + H₂O → ADP + Pi (inorganic phosphate) + E (Energy) Synthesis of ATP • Adding an inorganic phosphate to ADP can form ATP again in a condensation reaction. It occurs in 3 ways: • Photophosphorylation: In chlorophyll containing plant cells during photosynthesis • Oxidative Phosphorylation: In the mitochondria of plants and animal cells during electron transport • Substrate-level Phosphorylation: Plant and animal cells when phosphate groups are transferred from donor molecules to ADP making ATP • In the first two ATP is synthesised using energy released during electron transfer along an electron carrier chain
  21. 21. Roles of ATP ATP is the immediate energy source as its energy store is not long lasting due to the instability of the phosphate bonds Cells don’t store large quantities of ATP however ATP is rapidly re formed from ADP and inorganic phosphate easily making it go further ATP is better than glucose as it releases smaller more manageable quantities of energy The hydrolysis of ATP to ADP is a single reaction releasing energy immediately whereas the process for glucose is much longer ATP cannot be stored so is continuously made in the mitochondria, cells such as muscle fibres contain large mitochondria due to the required energy ATP as a source of energy • Metabolic Processes: Forming polysaccharides from monosaccharides, Polypeptides from amino acids and DNA/RNA from nucleotides • Movement: Provides energy for muscle contraction allowing the muscle filaments to slide over each other • Active Transport: ATP provides energy to change the shape of carrier proteins in plasma membranes allowing molecules to move against the concentration gradient • Secretion: Forms lysosomes needed for secretion of cell products • Activation of molecules: When a phosphate molecule is transferred from ATP to another it makes it more reactive lowering activation energy. This allows enzyme catalysed reactions to occur more readily
  22. 22. Absorption of Light Energy • Light energy is captured and is transferred to chlorophyll a molecules. • Electrons in the outer shell of the chlorophyll a molecule are excited. • The electrons are passed through a series of carrier molecules and are used to power, – Photolysis – Reduction of NADP – Photophosphorylation
  23. 23. 3.1 Photosynthesis Leaf Structure • Large surface area • Leaves minimise overlapping • Thin so short diffusion path • Transparent cuticle and epidermis let light through to photosynthetic mesophyll cells • Long narrow mesophyll cells packed with chloroplast • Large number of stomata able to open and close in light intensities • Air spaces allow diffusion of CO₂ and O₂ • Xylem brings water and phloem carries away sugars Photosynthesis Outline • 6CO₂ + 6H₂O → C6H12O + 6O2 • 1. Capturing light energy by chloroplast pigments e.g. chlorophyll • Light-dependent Reaction: Light converted into chemical energy, an electron flow is created and causes water to split (photolysis) into protons, electrons and oxygen. Products are reduced NADP, ATP and oxygen • Light-independent Reaction: Protons are used to reduce carbon dioxide to produce sugars and other organic molecules Structure of Chloroplast • Grana formed from thylakoids house the light dependent stage. They contain chlorophyll and also attach to each other via intergranal lamellae • Stroma is a fluid filled matrix where the light independent reaction occurs
  24. 24. ADP + P e- e- PHOTOPHOSPHORYLATION e- e- ATP e- PHOTOLYSIS light 2H2O Chlorophyll a 4H+ + e - + O2 THE LIGHT-DEPENDENT REACTION 4NADP  4NADPH
  25. 25. 3.2 The Light-Dependent Reaction When a substance loses electrons it is oxidised When a substance gains electrons it is reduced The Making of ATP • When chlorophyll absorbs light energy it causes a pair of electrons in it to become a higher energy level, they are in an excited state • The electrons then leave the chlorophyll and are taken up by an electron carrier • The chlorophyll has become oxidised and the electron carrier reduced • Via a series of oxidation-reduction reactions the electrons pass along the electron carriers as a transfer chain is formed in the membranes of the thylakoids • Each new carrier has a slightly lower energy level than the one before causing the electrons to lose energy • This energy is used to combine an inorganic phosphate molecule with ADP forming ATP Photolysis of Water • Due to the lose of electrons the chlorophyll they must be replaced • The electrons are replaced via water molecules being split using light energy • 2H₂O → 4H+ + 4e- +O₂ • The hydrogen ions are taken up by NADP causing it to be reduced • The reduced NADP and electrons from the chlorophyll enter the light independent reaction • Reduced NADP gives the plant a source of chemical energy • The oxygen by-product from the photolysis of water is diffused or used in respiration
  26. 26. Photolysis Water molecules are split using energy from excited electrons in chlorophyll a molecules. 2H2O  4H+ + 4e- + O2 Oxygen is released into the atmosphere. Hydrogen ions and electrons are now available to be used to produce a reducing agent.
  27. 27. Site of Light-Dependent Reaction Origin: Thylakoids of Chloroplast Adaptations of Chloroplast: • Thylakoid membranes provide a large surface area for chlorophyll attachment, electron carriers and enzymes • Network of proteins in the grana hold the chlorophyll in a precise manner for maximum absorption of light • Granal membranes have enzymes for ATP production • Contain both DNA and ribosomes so there is easy manufacture of proteins needed
  28. 28. Reduction of NADP  Electrons and Hydrogen ions produced during photolysis are used to reduce NADP to Reduced NADP (NADPH).  Excited electrons and hydrogen ions are transferred to NADP. NADP + H + + e-  NADPH  NADPH can donate electrons and hydrogen ions to carbon dioxide and so is a reducing agent.
  29. 29. 3.3 The Light-Independent Reaction It takes place in the stroma of the chloroplasts It doesn’t require light to occur ATP and reduced NADP are used to reduce carbon dioxide The Stages • Carbon dioxide from the atmosphere diffuses into the leaf through stomata and dissolves in water around the walls of the mesophyll cells. It then diffuses through the plasma membrane, cytoplasm and chloroplast membranes to the stroma • In the stroma, CO₂ combines with ribulose bisphosphate(RuBP) using an enzyme • Glycerate 3-phosphate (GP) is formed, 2 molecules per one combination • ATP and reduced NADP activate the GP into triose phosphate(TP) • The NADP is reformed and goes back to the light dependent reaction to be reduced again by accepting more hydrogen • Some TP is converted into useful organic substances such as glucose • Most TP is used to regenerate RuBP using ATP from the light dependent reaction
  30. 30. Photophosphorylation • Energy from the excited electrons is used to make ATP. • A phosphate group is added to ADP. ADP + P --energy from excited electrons  ATP
  31. 31. Products of the Light Dependent Stage • Photolysis – H+ ions – Electrons – Oxygen Used to produce NADPH • Photophosphorylation – ATP
  32. 32. The Calvin Cycle
  33. 33. Site of the Light-Independent Reaction The chloroplast is adapted for this reaction as: • The fluid of the stroma contains enzymes needed • The fluid surrounds the grana so the products can diffuse quickly to it • It contains both DNA and ribosomes so can easily manufacture proteins needed
  34. 34. 3.4 Factors affecting Photosynthesis Limiting Factors Light Intensity Carbon Dioxide Temperature • A limiting factor restricts the rate at which a process can occur • It is the slowest reaction that determines the overall rate of photosynthesis • ‘At any given moment, the rate of a physiological process is limited by the factor that is at its least favourable value’ • When light is the limiting factor photosynthesis is directly proportional to light intensity • As light intensity increases the volume of oxygen produced and carbon dioxide absorbed will increase till it balances the oxygen absorbed and carbon dioxide produced • This point is the compensation point due to no net exchange of gases into or out of the plant • When increasing light intensity has no effect on rate of photosynthesis there is another limiting factor • 0.1% CO₂ will give the optimum concentration for photosynthesis to occur • CO₂ concentration affects enzyme activity especially the enzyme that catalyses the combination of ribulose bisphosphate and carbon dioxide in the light independent reaction • From 0 to 25°C the rate of photosynthesis doubles for each 10°C • 25°C is the optimum temperature and after this the rate of photosynthesis declines due to enzymes becoming denatured • Photosynthesis isn't purely photochemical as if it was it wouldn’t be affected by temperature
  35. 35. The Light-Independent Reaction Does not require light energy. However, requires the products produced in the lightdependent reaction, therefore photosynthesis cannot occur without light energy. Takes place in the stroma. Enzyme controlled, therefore it is affected by temperature. Uses energy from ATP, and the electrons and hydrogen ions from NADPH to reduce CO2 to glucose.
  36. 36. Fixing Carbon Dioxide • Ribulose Biphosphate (RuBP), a 5 carbon molecule, combines with carbon dioxide via the enzyme RuBISCO. • This forms 2 molecules of glycerate-3-phosphate (GP), a 3 carbon organic acid.
  37. 37. Reducing glycerate-3-phosphate (GP)  NADPH and ATP from the lightdependent reaction are required for this stage.  NADPH transfers electrons and hydrogen ions to GP to form 2 molecules of Triose phosphate.  The energy for this is provided by the ATP.  The NADPH has now been oxidised back to NADP and can be reused in the light-dependent reaction.  The ATP has lost energy and so returns to ADP + P which can also be reused in the lightindependent stage.
  38. 38. Producing Glucose and Regenerating RuBP Producing Glucose Regenerating RuBP • For every 6 CO2 molecules entering the cycle, 12 Triose phosphates will be produced. • 2 of these molecules will be converted into glucose. • Of the 12 Triose phosphates that are produced, 10 will be used to regenerate RuBP.
  39. 39. Law of Limiting Factors: “ The overall rate of the process will be limited by the factor which is at the least favourable value” FACTORS AFFECTING THE RATE OF PHOTOSYNTHESIS
  40. 40. Light Intensity  At low light intensities, the rate of photosynthesis is directly proportional to the light intensity.  Because as more light becomes available, more chlorophyll molecules can absorb light so more electrons are excited leading to photolysis and photophosphorylation.  More ATP and NADPH are produced so the light-independent reactions can occur at a higher rate so more product is produced.  Eventually a maximum rate is reached and so increasing light intensity has no effect so the graph levels off.  This can be because all available chlorophyll molecules are absorbing light. Or some other factor is now the limiting factor.
  41. 41. Temperature  When light is not a limiting factor (i.e. high light intensities), increasing the temperature increases the rate of photosynthesis.  Above the optimum temperature, any further increase causes the rate to decrease rapidly.  Because the Calvin Cycle is enzyme controlled, when the temperature increases both enzymes and substrates gain kinetic energy, so more collisions occur, so more enzyme substrate complexes form, so more product forms.  When the temperature exceeds the optimum, the enzymes will denature and the specific shape of the active site will change and no longer be complementary to the substrate so fewer enzyme-substrate complexes can form.
  42. 42. Carbon Dioxide Concentration  At low CO2 levels an increase in concentration causes a directly proportional increase in the rate of photosynthesis.  A maximum rate is eventually reached and further increase has no effect and so the graph levels off.  This is because atmospheric CO2 levels are lower than the optimum value so when concentration is increased more CO2 is absorbed so more product is made.  Eventually, there is no more RuBP available to absorb anymore CO2 so there is no further effect.
  43. 43. IMPLICATIONS FOR COMMERCIAL GLASSHOUSE MANAGEMENT
  44. 44. What does glasshouse cultivation allow? • Better yields can be achieved because conditions for photosynthesis can be kept at an optimum. • Crops can be grown out of season all year providing a better economic return. • Crops can be grown in regions where they might not grow well naturally.
  45. 45. Factors to be Considered  For maximum yields to be achieved, limiting factors must be kept at an optimum because the faster the plant photosynthesises the more carbohydrates it produces which means the maximum yield will be achieved in the shortest time.  Carbon dioxide levels  High levels of CO 2 are the optimum however if the levels are too high over a long period of time then the stomata will close resulting in a drop in the rate of photosynthesis. A compromise level must therefore be used.  Temperature  An optimum temperature should be used to ensure that the plants photosynthesise rapidly without any damage to cells.  Water  Need to be well watered to ensure the stomata remain open to absorb CO 2. However the soil must not become waterlogged as it will reduce the uptake of mineral by active transport. The plants must not become to wet either as this will promote fungal disease to spread.  Light  Artificial lighting is used when natural light intensity falls. Specific wavelengths are chosen so they are absorbed by the plants (i.e. red and blue).  Minerals  Soil must be supplemented with essential minerals. Potassium is particularly important in stomatal mechanisms and so must be kept at an optimum.
  46. 46. AQA A2 Biology Unit 4 Respiration
  47. 47. Specification 3.4.4 In respiration, glycolysis takes place in the cytoplasm and the remaining steps in the mitochondria. ATP synthesis is associated with the electron transfer chain in the membranes of mitochondria. Aerobic Respiration glycolysis takes place in the cytoplasm and involves the oxidation of glucose to pyruvate with a net gain of ATP and reduced NAD pyruvate combines with coenzyme A in the link reaction to produce acetylcoenzyme A in a series of oxidationreduction reactions the Krebs cycle generates reduced coenzymes and ATP by substrate-level phosphorylation, and carbon dioxide is lost Aerobic Respiration Conc acetylcoenzyme A is effectively a two carbon molecule that combines with a four carbon molecule to produce a six carbon molecule which enters the Krebs cycle synthesis of ATP by oxidative phosphorylation is associated with the transfer of electrons down the electron transport chain and passage of protons across mitochondrial membranes. Anaerobic respiration Glycolysis followed by the production of ethanol or lactate and the regeneration of NAD in anaerobic respiration.
  48. 48. Definitions • • • • • • • • • • Hydrolysis: Breaking down of large molecules into smaller ones by the addition of water Activation Energy: Energy required to bring about a chemical reaction Oxidation: Lose of Electrons Glycolysis: First part of cellular respiration in which glucose is broken down anaerobically in the cytoplasm to 2 molecules of pyruvate Substrate-Level Phosphorylation: The formation of ATP by the direct transfer of a phosphate group from a reactive intermediate to ADP Aerobic: Connected with the presence of oxygen, aerobic respiration requires oxygen to release energy from glucose and other foods Adenosine Triphosphate: An activated nucleotide found in all living cells that acts as an energy carrier. Redox: Reaction in which oxidation and reduction take place Krebs Cycle: Series of aerobic biochemical reactions in the matrix of the mitochondria of most eukaryotic cells by which energy is obtained through the oxidation of acetylcoenzyme A produced in the breakdown of glucose NAD: (Nicotinamide adenine dinucleotide phosphate) Molecule that carries electrons and hydrogen ions during aerobic respiration
  49. 49. 4.1 Respiration Overview Glucose cannot be used directly by cells as an energy source so they use ATP There are two different forms of respiration: • Aerobic Respiration: requires oxygen and produces carbon dioxide, water and much ATP • Anaerobic Respiration ((fermentation): Takes place in the absence of oxygen and produces lactate (inn animals) or ethanol and carbon dioxide in plants, very little ATP is produced Aerobic Respiration steps: • Glycolysis: Splitting of the 6 carbon glucose molecule into 2 3carbon pyruvate molecules • Link Reaction: Conversion of the 3-carbon pyruvate into carbon dioxide and a 2-carbon molecule called acetylcoenzyme A • Krebs Cycle: Introduction of acetylcoenzyme A into a cycle of oxidation-reduction reactions that yield some ATP and a large number of electrons • Electron Transport Chain: Use of the electrons produced in the Krebs Cycle to synthesis ATP with water produced as a byproduct
  50. 50. Glycolysis Glycolysis is the initial stage in both aerobic and anaerobic respiration Occurs in the cytoplasm of all living cells A hexose sugar is split into 2 molecules of 3-carbon pyruvate It has four stages: Energy Yield: • Activation of Glucose by phosphorylation: Glucose is made more reactive by adding 2 phosphate molecules, these come from the hydrolysis of 2 ATP molecules to ADP. This provides energy to activate the glucose as the activation energy has been lowered • Splitting of the Phosphorylated glucose: Each glucose molecule is split into 2 3-carbon molecules known as triose phosphate • Oxidation of Triose Phosphate: Hydrogen is removed from each triose phosphate molecule and transferred to a hydrogen-carrier molecule (NAD) to form reduced NAD • Production of ATP: Enzyme controlled reactions convert each triose phosphate into another 3-carbon molecule called pyruvate, 2 molecules of ATP are regenerated from ADP • 2 molecules of ATP • 2 molecules of reduced NAD • 2 Molecules pyruvate As glycolysis occurs in the cytoplasm of cells it doesn’t require an organelle or membrane for it to occur It doesn’t require oxygen and without oxygen pyruvate is converted to lactate or ethanol by anaerobic respiration
  51. 51. Glycolysis  Glycolysis takes place in the cytoplasm of the cell.  Glucose is first phosphorylated by 2 phosphate groups from 2 molecules of ATP to produce 2 molecules of glyceraldehyde-3-phosphate (GALP).  GALP is then oxidised and dephosphorylated into pyruvate.  In this process, the phosphate groups are transferred to ADP producing 2 molecules of ATP. A hydrogen is transferred to a molecule of NAD producing NADH.  The net yield of glycolysis per glucose is  2ATP  2NADH  2 pyruvate  The pyruvate produced then diffuses into the mitochondria. 1 x Glucose 2ATP 2ADP + 2P 2 x Glyceraldehyde 3-phosphate 2NAD 4ADP + 4P 2NADH 4ATP 2 x Pyruvate
  52. 52. 4.2 The Link Reaction For pyruvate molecules to enter the Krebs cycle they need to by oxidised Occurs in the mitochondria Pyruvate produced in the cytoplasm is actively transported into the matrix of mitochondria Pyruvate undergoes a series of reactions: • Hydrogen is removed from the pyruvate, the hydrogen is accepted by NAD to form reduced NAD • 2-carbon molecule, acetyl group, is formed and then combines with coenzyme A ((CoA) to produce acetylcoenzyme A • A carbon dioxide molecule is formed from each pyruvate Pyruvate + NAD + CoA → acetyl CoA + reduced NAD + CO₂
  53. 53. The Link Reaction  Takes place in the matrix.  Pyruvate undergoes oxidative decarboxylation.  Oxidation 2 x Pyruvate NAD  Electrons and hydrogen from the pyruvate are transferred to NAD producing NADH.  Decarboxylation  Carbon dioxide is removed which converts the pyruvate into acetate.  The acetate then combines with CoenzymeA to produce Acetyl CoenzymeA.  Since 2 molecules of pyruvate were produced in glycolysis, the net yield of the link reaction per glucose is  2 Acetyl CoenzymeA  2NADH  2 Carbon dioxide NADH Carbon dioxide CoenzymeA Acetyl CoenzymeA
  54. 54. The Krebs Cycle Series of oxidation-reduction reactions in the matrix of mitochondria • 2-carbon acetylcoenzyme A from the link reaction combines with 4-carbon molecule to produce a 6-carbon molecule • The 6-carbon molecule loses carbon dioxide and hydrogen to give a 4-carbon Process: molecule and a single ATP molecule produced as a result of substrate-level phosphorylation • The 4-carbon molecule can now be combined with another acetylcoenzyme A to repeat the cycle • Reduced coenzymes e.g. NAD/FAD have the potential to produce ATP molecules Products: • 1 molecule of ATP • 3 molecules of carbon dioxide Due to 2 pyruvate molecules being produced from each original glucose the yield of a single glucose molecule is double the quantities above Coenzymes: some enzymes require to function Significance of the Krebs Cycle • Major role in photosynthesis and respiration as carry hydrogen atoms from one molecule to another e.g. • NAD, important throughout respiration • FAD, important in the Krebs cycle • NADP, important in photosynthesis • NAD is the most important carrier, it works with dehydrogenase enzymes that catalyse the removal of hydrogen ions from substrates and transfers them to other molecules such as hydrogen carriers involved in oxidative phosphorylation • It breaks down macromolecules into smaller ones e.g. pyruvate into carbon dioxide • It produces hydrogen atoms carried by NAD to the electron transport chain for oxidative phosphorylation . This leads to the production of ATP for metabolic energy in the cell • It regenerates 4-carbon molecule that combines with acetylcoenzyme A • It is a source of intermediate compounds used by cells to manufacture substances such as fatty acids and chlorophyll
  55. 55. The Krebs Cycle • • • • • Takes place in the matrix. Closed cycle of enzyme controlled reactions. Provides a continuous supply of reduced electron carriers for the electron transport chain. AcetylCoA combines with a 4-C compound to produce citric acid, a 6-C compound. The citric acid then undergoes – – • • A decarboxylation reaction which removes carbon dioxide. A series of oxidation reactions which remove hydrogen ions and electrons. H + ions and e – are picked up by NAD and FAD and they become NADH and FADH. At the end of the cycle the 4-C compound is recycled so the cycle can continue. Since each glucose molecule produced 2 molecules of pyruvate and so 2 molecules of AcetylCoA, the yield per glucose for the Krebs cycle is – – – – NADH 4 carbon dioxide 2FADH 6NADH 2ATP ADP NADH ATP FADH NADH
  56. 56. 4.3 Electron Transport Chain Occurs in the mitochondria Enzymes are attached to the cristae that are involved in the electron transport chain Synthesis of ATP Importance of Oxygen • Hydrogen atoms produced in glycolysis and the Krebs cycle combine with coenzyme NAD and FAD that are attached to the cristae • Reduced NAD and FAD donate the electrons of the hydrogen atom to the first molecule in the electron transport chain • This releases the protons from the hydrogen atoms and these are actively transported across the inner mitochondrial membrane • The electrons pass along the chain via oxidation-reduction reactions in which they lose energy that combines ADP and an inorganic phosphate to make ATYP, remaining energy is given off as heat • The protons accumulate in the space between the mitochondrial membranes before they diffuse back into the matrix through special protein channels • At the end electrons combine with the protons and oxygen to form water • It is the final acceptor of hydrogen atoms • Without it the hydrogen ions and electrons would ‘back up’ along the chain and respiration would cease • Cyanide is a non-competitive inhibitor of the final enzyme in the electron transport chain • It catalyses the addition of the hydrogen ions and electrons to oxygen to form water • Its inhibition causes hydrogen ions and electrons to accumulate on the carriers stopping cellular respiration
  57. 57. Electron Transport Chain  Found on the cristae of the mitochondria which provide a large surface area for this to take place.  The electron carriers are arranged in descending energy levels.  When electrons pass through the carriers, the energy released is used to move hydrogen ions from the matrix into the intermembrane space.  This creates a large concentration gradient of H+ ions and so they diffuse back into the mitochondrial membrane by diffusion via ATP synthase.  As the H+ ions diffuse through the enzyme, they attach P groups to ADP to produce ATP.  At the end of the chain, the electrons are picked up by the terminal electron acceptor, which is oxygen, to produce water. - + 2H + + ½O  H O 2e 2 2  This process is called oxidative phosphorylation.
  58. 58. 4.4 Anaerobic Respiration Without oxygen the Krebs Cycle and the Electron Transport Chain cannot occur Only glycolysis is a source of ATP, for it to continue its products of pyruvate and hydrogen must be constantly removed The hydrogen must be released from the reduced NAD in order to regenerate NAD as if it wasn’t converted no NAD could take up the newly produced hydrogen from glycolysis and it would stop The replenishment of NAD is achieved by pyruvate accepting hydrogen from the reduced NAD
  59. 59. Production of Ethanol • Bacteria, fungi and plants can produce ethanol • The pyruvate molecule formed in glycolysis loses a molecule of carbon dioxide and accepts hydrogen from reduced NAD to produce ethanol • Yeast is grown in anaerobic conditions to produce ethanol for brewing • Pyruvate + reduced NAD → Ethanol + Carbon dioxide + NAD Production of Lactate • Anaerobic respiration I animals leads to lactate production in order to overcome temporary shortage of oxygen • Lactate production occurs most commonly in muscles as a result of strenuous exercise as there is not enough oxygen being supplied causing an oxygen debt • Reduced NAD must be removed in order for energy to be released • This is achieved as each pyruvate molecule produced takes up 2 hydrogen atoms from the reduced NAD produced in glycolysis to form lactate • Lactate needs to be oxidised back to pyruvate • It can either further to release energy or converted into glycogen • Lactate build up can cause cramp and muscle fatigue. Muscles do have a certain tolerance however it has to be removed by the blood and taken to the liver to be converted to glycogen • Pyruvate + reduced NAD → lactate + NAD Energy Yields • In anaerobic respiration, pyruvate is converted to either ethanol or lactate. • Therefore in anaerobic respiration neither the Krebs cycle nor the electron transport chain can take place • The only ATP that can be produced anaerobic respiration is formed by glycolysis which is a very small amount compared to aerobic respiration
  60. 60. 1 x Glucose 2NAD 2ADP + 2P 2NADH 2ATP 2 x Pyruvate ANAEROBIC RESPIRATION 2NADH 2NAD 2 x Lactic Acid
  61. 61. Anaerobic Respiration When oxygen isn’t available, the electron transport chain cannot operate so the initial supply of NAD run out. To regenerate this, pyruvate produced during glycolysis must be reduced. Pyruvate is converted into lactic acid in animal cells. Pyruvate + NADH  Lactic Acid The net yield from anaerobic respiration is simply the 2ATP produced in glycolysis and is therefore much less energy efficient. In some plants and microbes, pyruvate is converted into ethanol. Pyruvate + NADH  Ethanol + Carbon Dioxide + NAD
  62. 62. AQA A2 Biology Unit 4 Nutrient Cycles
  63. 63. Specification 3.4.6 Chemical elements are recycled in ecosystems. Microorganisms play a key role in recycling these elements. Candidates should be able to analyse, interpret and evaluate data relating to evidence of global warming and its effects on the yield of crop plants, the life-cycles and numbers of insect pests, the distribution and numbers of wild animals and plants. Candidates should be able to analyse, interpret and evaluate data relating to eutrophication. Nutrient cycles The role of microorganisms in the carbon and nitrogen cycles in sufficient detail to illustrate the processes of saprobiotic nutrition, ammonification, nitrification, nitrogen fixation and denitrification. Carbon The importance of respiration, photosynthesis and human activity in giving rise to short-term fluctuation and longterm change in global carbon dioxide concentration. The roles of carbon dioxide and methane in enhancing the greenhouse effect and bringing about global warming. Nitrogen The environmental issues arising from the use of fertilisers. Leaching and eutrophication.
  64. 64. Definitions • • • • • • • • • • • • Active Transport: Movement of a substance across a membrane from a region of low concentration to high concentration using ATP Aerobic: In the presence of oxygen Anaerobic: Without oxygen Biomass: Total mass of living material in a specific area at a given time, usually measured as dry mass since water value is variable Consumers: Organism that obtains energy by eating another Decomposer: An organism, e.g. fungus that breaks down organic material. Ecosystem: Unit in ecology made up of all interacting biotic and abiotic factors in a specific area Greenhouse Gas: Such as methane and carbon dioxide, they cause heat to be trapped in the atmosphere raising the Earth’s temperature Niches: All conditions and resources required for an organism to survive, reproduce and maintain population Oxidation: Chemical reaction causing the loss of electrons Producers: Organism that synthesises organic molecules from simple inorganic ones Saprobiotic Microorganisms (Saprophyte): Organism that obtains food from dead or decaying remains of other organisms
  65. 65. Basic Nutrients Cycle • The flow of nutrients such as carbon and nitrogen is cyclic When both the producer and consumer die saprobiotic microorganisms break down the molecules releasing the nutrients Nutrients taken up by producers (plants) as simple inorganic molecules The nutrients are then passed along a food chain Producers incorporates the nutrient into complex organic molecules The producer is eaten and nutrients pass to the consumers
  66. 66. 6.1 The Carbon Cycle The main source of carbon for terrestrial organisms is carbon dioxide in the atmosphere Photosynthetic organisms remove it from the air to form macromolecules e.g. carbohydrates, fats and proteins Respiration returns carbon dioxide back to the air The concentration of CO₂ is higher at night than day due to no photosynthesis occurring while respiration still occurs
  67. 67. The Increase in Carbon Dioxide Main Reasons due to human activities: • Combustion of Fossil Fuels: Coal, oil and peat releases CO₂ previously trapped • Deforestation: Removes photosynthesising biomass so less CO₂ is removed CO₂ is a greenhouse gas and contributes to global warming The ocean is a CO₂ sink so keeps it constant When organisms die Saprophytes break them down into small soluble molecules using enzymes • The decomposers then absorb the molecules via diffusion The carbon is then released as CO₂ during respiration of the decomposer When decay is prevented fossils are formed
  68. 68. The Carbon Cycle Diagram
  69. 69. 6.2 The Greenhouse Effect and Global Warming The Greenhouse Effect • Natural process that occurs all the time • Due to solar radiation from the sun reaching the earth • Greenhouse gases trap the heat in the Earth’s atmosphere causing it to heat up Greenhouse Gases • The major greenhouse gas is CO₂ which is increasing due to human activities • Methane is also produced when microorganisms break down organic molecules , it occurs in two situations: • Decomposers break down dead remains of organisms • Microorganisms in intestines of primary consumers e.g. cattle digest food Global Warming • Due to the layer of greenhouse gases building up it traps the heat from the sun causing the Earth to heat up
  70. 70. Consequences of Global Warming Changes in temperature and precipitation, the timing of seasons and frequency of extreme events e.g. storms Climate change will effect niches available due to organisms being adapted to particular niches Animals could migrate to new areas causing competition and loss of native species Melting ice gap could cause extinction of wild plants and animals e.g. polar bears and sea levels will rise Low land would be flooded and sea water would extend further up rivers making cultivation difficult Droughts could occur due to higher temperatures meaning xerophytes could only survive Greater rainfall would occur in some areas Insect lifecycles will be altered and due to them carrying human and crop pathogens tropical diseases could spread toward poles Benefit could be more rainfall filling reservoirs, higher temperatures causing higher rate of photosynthesis so more productivity and a larger harvest
  71. 71. 6.3 The Nitrogen Cycle All living organisms require a source of nitrogen to form nucleic acids and proteins Plants take most of their nitrogen up via nitrate ions (NO₃-) from the soil The ions are absorbed by active transport from the root hairs Animals obtain their nitrogen compounds by eating the plants Nitrate ions are soluble When plants and animals die decomposition occurs and the nitrates are restored to the soil
  72. 72. The Stages of the Nitrogen Cycle Ammonification • The production of ammonia from organic ammonium compounds e.g. urea, proteins and nucleic acids • Saprobiotic microorganisms e.g. fungi feed on these materials releasing ammonia which forms ammonium ions in the soil • This is where nitrogen returns to non living components of the ecosystem Nitrification • Ammonium ions to nitrate ions is an oxidation reaction so releases energy • It is carried out by nitrifying bacteria in two stages: • 1. Oxidation of ammonium ions to nitrite ions (NO₂¯) • 2. Oxidation of nitrite ions to nitrate ions (NO₃¯) • Nitrifying bacteria require oxygen to carry out the conversions so the soil needs to have air spaces • Farmers keep soil light and aerated by ploughing and having good drainage Nitrogen Fixation • Nitrogen gas is converted to nitrogen containing compounds • 1. Free living nitrogen fixing bacteria reduce gaseous nitrogen to ammonia to manufacture amino acids, when the bacteria dies and decay they release the nitrogen compounds • 2. Mutualistic nitrogen fixing bacteria live in nodules on roots of plants and they obtain carbohydrates from the plant while in return the plant acquires amino acids from the bacteria Denitrification • When soil is waterlogged there is a shortage of oxygen and the type of microorganism present changes • Fewer aerobic nitrifying and nitrogen fixing bacteria are found meaning more anaerobic denitrifying bacteria are present • This bacteria converts soil nitrates into gaseous nitrogen reducing availability of nitrogen containing compounds for plants • To prevent the build up of denitrifying bacteria the soil has to be well aerated
  73. 73. 6.4 Use of Natural and Artificial Fertilisers Intensive food production makes large demands on the soil Due to this the minerals are removed from the soil, in agriculture the remains of the consumer are rarely returned to the same area so mineral ions fall The mineral ions need to be replenished so fertilisers are added • Natural (organic): consist of dead/decaying remains as well as animal waste • Artificial (inorganic): Mined from rocks and deposits then converted into different forms to give the appropriate balance of minerals , compounds contain nitrogen, phosphorus and potassium
  74. 74. Fertilisers Increasing Productivity Plants require minerals for growth, nitrogen is needed for proteins and DNA With nitrogen plants grow taller and have a greater leaf area This increases the rate of photosynthesis and improves crop productivity
  75. 75. 6.5 Environmental Consequences of using Nitrogen Fertilisers Effects of Nitrogen Fertilisers • Nitrogen is essential for proteins and growth and causes the increase in leaf area • This increases the rate of photosynthesis and improves crop productivity The nitrogen containing fertilisers have bad effects to: • Reduced species diversity as nitrogen rich soils favour growth of grasses so they out compete other species that then die • Leaching leads to pollution of watercourses • Eutrophication caused by leaching of fertiliser into watercourses
  76. 76. Leaching and Eutrophication Leaching • The process by which nutrients are removed from the soil • Rain water will dissolve soluble nutrients e.g. nitrates and carry them into the soil beyond plant roots • The leached nitrates reach the watercourses e.g. rivers that drain into freshwater lakes • They can harm drinking water, prevent efficient oxygen transport in babies and cause stomach cancer • The leached nitrates are harmful to environment as they cause eutrophication Eutrophication • The process by which nutrients build up in bodies of water • Most rivers contain low nitrate levels so it is a limiting factor for plant/algae growth • Nitrate concentration increases due to leaching so the plants grow exponentially • Algae grow at the surface so the upper layers of water become densely populated with algae, ‘algae bloom’ • The layer absorbs light and prevents it from reaching the lower depths • Light becomes the limiting factor for growth so plants at deeper depths die • The lack off dead plants and algae is no longer limiting for the growth of saprobiotic algae so they grow exponentially • Saprobiotic bacteria require oxygen for respiration creating a demand for oxygen • The concentration of oxygen in the water is reduced and nitrates are reduced from decaying organisms • Oxygen then becomes the limiting factor for aerobic organisms e.g. fish so they die • Without aerobic organisms there is less competition for anaerobic organisms • These organisms further decompose dead material realising more nitrates and toxic waste like hydrogen sulphide • Animal slurry, human sewage, ploughing and artificial fertilisers cause leaching
  77. 77. AQA A2 Biology Unit 4 Ecological Succession
  78. 78. Specification 3.4.7 Ecosystems are dynamic systems usually moving from colonisation to climax communities in the process of succession. Succession Succession from pioneer species to climax community. At each stage in succession, certain species may be recognised which change the environment so that it becomes more suitable for other species. The changes in the abiotic environment result in a less hostile environment and changing diversity. Conservation of habitats frequently involves management of succession. Candidates should be able to • use their knowledge and understanding to present scientific arguments and ideas relating to the conservation of species and habitats • evaluate evidence and data concerning issues relating to the conservation of species and habitats and consider conflicting evidence • explain how conservation relies on science to inform decision-making.
  79. 79. Definitions • Ecosystem: More or less a self-contained functional unit in ecology made up of all the biotic and abiotic factors of a specific area • Abiotic: An ecological factor that makes up part of the non-biological environment of an organism e.g. temperature • Biotic: An ecological factor that makes up the living environment e.g. food • Communities: The organisms of all species that live in the same area • Deciduous: Plants that shed their leaves in one season • Habitats: The place where an organism lives, characterised by physical conditions and the species of other organisms present • Climax Community: The organisms that make up the final stage of ecological succession • Biodiversity: The range and variety of living organisms within a particular area • Biomass: The total mass of a living material in a specific area at a given time, usually measured as dry mass as amount of water is variable • Conservation: The management of the Earth’s natural resources
  80. 80. 7.1 Succession Ecosystems constantly change, this is known as succession The first stage of succession is the colonisation of an inhospitable environment by the pioneer species Pioneer Species Adaptations: Succession Stages Succession Features: • Product vast quantities of wind dispersed seeds/spores • Rapid germination of seeds on arrival • Ability to photosynthesise • Ability to fix nitrogen from the atmosphere • Tolerant of extreme conditions • Over these stages the environment becomes more hospitable and new species begin to grow which can outcompete other species • The pioneer species e.g. lichen, grow in inhospitable environments and as time progresses the lichen die and decompose producing nutrients to support the community • Lichens have changed the abiotic environment by creating soil and nutrients • Mosses are the next followed by ferns causing an increase in organic matter, due to the dying plants the soil becomes thicker • The hospitability is increased till the ultimate community is formed (climax community) • Due to the variation of plants a variation of animals is also increased • Non-living environment becomes less hostile due to nutrients being increased • Greater number and variety of habitats • Increased biodiversity • More complex food webs • Increased biomass
  81. 81. Climax Communities • Have a stable equilibrium with the climate • Abiotic factors determine the dominate species in the community Secondary Succession • If land has been cleared for agriculture or a forest fire the process of succession still occurs • It is a faster process as spores and seeds remain alive in the soil and there is an influx of animals and plants via migration • There is no need for a pioneer species
  82. 82. 7.2 Conservation of Habitats Conservation involves active intervention from humans to maintain biodiversity Reasons for conservation: • Ethical: Species should be allowed to coexist with humans • Economic: Living organisms have a large pool of genes that could be valuable. Long term productivity is greater if ecosystems are maintained • Cultural and Aesthetic: Habitats and their organisms enrich our lives Managing Succession • Many of the organisms present in the series of succession are no longer present at the climax community • Due to being outcompeted or their habitat being no more the species often migrate • In order to combat this problem succession is stopped e.g. the land my be burnt or grazed on by sheep stopping tree saplings from growing • If the factor preventing further succession is removed then the climax community will grow in secondary succession

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