1 4.1.

1 Communication Context and exemplification Assessable learning outcomes Organisms use chemical and electrical systems to monitor and respond to any deviation from the bodys steady state. Candidates should be able to: (a) outline the need for communication systems within multicellular organisms, with reference to the need to respond to changes in the internal and external environment and to coordinate the activities of different organs; Animals increase their chances of survival by responding to changes in their external environment. These can be changes over time, eg. winter to summer fur based on long term temperature or short term eg. changing the size of pupils based on light intensity. Internal environments can change too Internal environments can change too: the build up of carbon dioxide as a result of respiration changes the pH of the tissue fluid and this change in pH can denature enzymes and so inhibit their activity. Multicellular organisms need to coordinate different organs, so this requires a good communication system which will: cover the whole body, enable cells to communication with each other, enable specific communication, enable rapid communication and enable both short and long term responses. (b) state that cells need to communicate with each other by a process called cell signalling; Cells need to communicate with each other by a process called cell signalling. (c) state that neuronal and hormonal systems are examples of cell signalling; Neuronal and hormonal systems are examples of cell signalling. (d) define the terms negative feedback, positive feedback and homeostasis; Negative feedback-

2 A process in which any change in a parameter brings about the reversal of that change so that the parameter is kept fairly constant. This is in the context of glucose control.

Positive feedbackA process in which any change in a parameter brings about an increase in that change. (Does not really occur in homeostasis, as it pushes parameters further and further from the normal values. It occurs in contractions when giving birth, oxytocin stimulates more oxytocin, oxytocin also stimulates contractions and more oxytocin to stimulate more oxytocin and more contractions.

3 Homeostasis-

(e) explain the principles of homeostasis in terms of receptors, effectors and negative feedback; If there is a change in an internal parameter away from the narrow normal limits, it is detected by receptors (often in the hypothalamus, or can be peripheral receptors). The communication system transmits an impulse from the receptor to the effectors and the effectors act to reverse the charge in the parameter and to return it to the normal range.

4 (f) describe the physiological and behavioural responses that maintain a constant core body temperature in ectotherms and endotherms, with reference to peripheral temperature receptors, the hypothalamus and effectors in skin and muscles. IN ENDOTHERMS: Can control own temperature both behaviourally and physiologically.

IN ECTOTHERMS: To maintain a constant core body temperature, ectotherms have physiological and behavioural responses; Physiological They can try to expand their surface area to absorb more heat from the sun, eg. the horned lizard expands its ribcage and the frilled lizard spreads out its frill. Locusts increase their abdominal breathing movements to increase water loss when hot to lose more heat by evaporation. Behavioural Snakes lie in the sun to warm up. Locusts can orient themselves to expose the most area possible to the sun when cold and conversely orient themselves so the minimum area possible is exposed to the sun when hot. Lizards can hide in burrows to avoid the sun so they absorb less heat when hot.

4.1.2 Nerves Context and exemplification Assessable learning outcomes In receptors, the energy of a stimulus is transferred into energy in an action potential in a neurone. Transmission between neurones takes place at

6 synapses. Candidates should be able to: (a) outline the roles of sensory receptors in mammals in converting different forms of energy into nerve impulses; Receptors are cells that respond to stimuli and act as biological transducers. Receptor Rod/Cone cells in the retina Taste buds on tongue Olfactory cells in nose Pacinian corpusles in skin Meissners corpusles in skin Ruffinis endings in skin Proprioceptors in muscles Sense Sight Taste Smell Pressure Touch Temperature Placement of limbs Form in which the energy is received Light Chemical potential Chemical potential Movement and pressure Movement and pressure Heat Stretch (mechanical displacement)

(b) describe, with the aid of diagrams, the structure and functions of sensory and motor neurones;

Motor Neurone Motor has dendrites on cell body Motor has terminal cell body Motor has cell body in the CNS Motor has no dendron Motor has a longer axon

Sensory Neurone Sensory doesnt have dendrites on the cell body Sensory has it in the middle Sensory has it in the PNS Sensory does have a Dendron Sensory has a shorter axon

(c) describe and explain how the resting potential is established and maintained; The resting potential difference across the membranes of neurones is -60 or -70 millivolts. (The membrane is polarised at rest.) Na+/K+ pumps in the membrane pump 3Na+ out of the membrane for every 2K+ pumped in. Membrane is impermeable to Na+ so it cant leak in, but permeable to K+ so K+ can leak out. Neurone contains negatively charged proteins which the membrane is impermeable to.

(d) describe and explain how an action

9 potential is generated; At the start the membrane is at its resting state (-60mV compared to the outside). Polarised. The Na+ ions open and some Na+ ions diffuse out. The membrane depolarises- it becomes less negative with respect to the outside and reaches the threshold potential of -50mV. Voltage-gated sodium ion channels open and many Na + ions enter. As more Na+ ions enter, the more positively charged the cell becomes, compared to the outside. The potential difference across the membrane reaches +40mV. The inside is now positive compared to the outside. The Na+ ion channels shut and the K+ ion channels open. K+ ions diffuse out of the cell, bringing the potential difference back to negative compared with the outside- repolarisation. The potential difference overshoots slightly, making the cell hyperpolarised. The original potential difference is restored, so the cell returns to its resting state. (e) describe and explain how an action potential is transmitted in a myelinated neurone, with reference to the roles of voltage-gated sodium ion and potassium ion channels;

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Myelination of nerves means that depolarisation only occurs at the nodes of Ranvier, so the local circuits are longer as sodium ions flow between the nodes of Ranvier because they cannot pass through the Schwann cells as they are insulated with myelin. Non-myelinated neurones can only do continuous conduction; myelinated neurones can do salutatory conduction.

11 (f) interpret graphs of the voltage changes taking place during the generation and transmission of an action potential;

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(g) outline the significance of the frequency of impulse transmission; Action potentials are the same size no matter their intensity so stronger signals have a higher frequency of action potentials than weaker signals which have a lower frequency of action potentials. A stimulus at the higher intensity will cause the sensory neurons to produce more generator potentials. More frequent action potentials in the sensory neurone More vesicles released at the synapse A higher frequency of action potentials in the postsynaptic neurone A higher frequency of signals to the brain A more intense stimulus Refractory period stuff:

(h) compare and contrast the structure and function of myelinated and non-myelinated neurones;

13 Myelinated Neurones 100 ms-1 transmission speed Up to 1m transmission distance Fast response time Used in movement 1/3 of all neurones One neurone is surrounded by one Schwann cell, wrapped round many times Non-Myelinated Neurones 2-20 ms-1 transmission speed Mm or cm transmission distance Slow response time Used in breathing or digestion 2/3 of all neurones Many neurones are surrounded by one Schwann cell

(i) describe, with the aid of diagrams, the structure of a cholinergic synapse;

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(j) outline the role of neurotransmitters in the transmission of action potentials;

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Acetylcholine diffuses across the synaptic cleft and it binds with the receptors on the post-synaptic membrane, opening Na+ channels which allows Na+ ions to flood in, setting up another action potential. Acetylcholinesterase breaks down acetylcholine into acetate and choline to prevent the acetylcholine from constantly stimulating the receptors on the postsynaptic membrane, and the acetate and choline diffuse back to the presynaptic membrane, the choline is taken back into the presynaptic neurone and combined with acetyl CoA to form acetylcholine once more. (k) outline the roles of synapses in the nervous system.

4.1.3 Hormones

16 Context and exemplification Assessable learning outcomes The ways in which specific hormones bring about their effects are used to explain the action of hormones. Treatment of diabetes is used as an example of the use of medical technology in overcoming defects in hormonal control systems. The control of heart rate is used as an example of the integration of nervous and hormonal control. Candidates should be able to: (a) define the terms endocrine gland, exocrine gland, hormone and target tissue; Endocrine gland- they secrete hormones directly into the blood. They are ductless. Eg. thyroxine, ADH, insulin.

Exocrine gland- they secrete useful molecules into a duct that carries the molecules outside the body. Eg. bile, saliva, sweat.

Hormone-Hormones are chemical messengers secreted directly into the blood from ductless endocrine glands. Target tissue-a group of cells that have receptors embedded in the plasma membrane that are complementary in shape to the specific hormone molecules. Only these cells will respond to the specific hormone. (b) explain the meaning of the terms first messenger and second messenger, with reference to adrenaline and cyclic AMP

17 (cAMP); First messenger is the molecule that transmits a message around the body. Eg. adrenaline. This stimulates a second messenger inside the target cell. Second messenger transmits a signal inside the cell and activates a series of enzyme controlled reactions. eg. cAMP. (c) describe the functions of the adrenal glands; There are a pair of adrenal glands situated anterior to the kidneys. There is a cortex and a medulla. The outer cortex forms 80% of the gland. The cortex produces 2 types of steroid hormones: 1. Mineralocorticoids, eg. aldosterone. Helps control the concentrations of Na+ and K+ ions in the blood. 2. Glucocorticoids, eg. cortisol. Help control the metabolism of carbohydrates and proteins in the liver. The adrenal medulla is activated by sympathetic neurones. Secretes adrenaline and noradrenaline. Both of these relax smooth muscle in the bronchioles, increase cardiac output (increase stroke volume and heart rate), causes general vasoconstriction (raises blood pressure), stimulates conversion of glycogen to glucose, dilates the pupils, increases mental awareness, inhibits the action of the gut and causes body hair to erect. (d) describe, with the aid of diagrams and photographs, the histology of the pancreas, and outline its role as an endocrine and exocrine gland;

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It is part endocrine and part exocrine. It is endocrine because it secretes the hormones insulin and glucagon directly into the blood. At the same it is still exocrine it secretes pancreatic enzymes, including the enzymes amylase, trypsin. Islets of Langerhans are the pieces of endocrine tissue in the pancreas. The alpha cells secrete glucagon and the beta cells secrete insulin. (e) explain how blood glucose concentration is regulated, with reference to insulin, glucagon and the liver;

19 Low blood glucose concentration detected by the alpha cells in the pancreas. Glucagon is secreted in response to this. It travels in the blood and then binds to receptors on the cell membranes of liver cells.

(f) outline how insulin secretion is controlled, with reference to potassium channels and calcium channels in beta cells; Cells allow diffusion of K+ ions out of the cell so the (resting) potential difference across the cell surface membrane is -65mV. If glucose levels around the cell are high, glucose diffuses into the cell. An enzyme, called glucokinase, phosphorylates the glucose into glucose phosphate. The glucose phosphate is used in respiration to make ATP. The increased levels of ATP cause the K+ channels to shut. The K+ ions cannot diffuse out and so the membrane potential difference changes to -30mV. Ca2+ ion channels which are normally shut now open and Ca 2+ ions diffuse into the cell. The influx of Ca2+ ions leads to insulin-loaded vesicles to move towards the cell surface membrane and fuse with it releasing the insulin by exocytosis. (g) compare and contrast the causes of Type 1 (insulin-dependent) and Type 2 (noninsulin-dependent) diabetes mellitus; Type 1= juvenile onset, develops when the beta cells of the pancreas are incapable of secreting sufficient insulin. It may be due to an immune response where white blood cells attack recognise the self antigens on the beta cells as foreign and attack them, killing or damaging them and meaning that not enough insulin is secreted to control insulin levels. Type 2= late onset, this is where the pancreas do produce insulin but the receptors on the liver and muscle cells do not respond. Uptake of glucose into the cells of a diabetic is slow.

20 (h) discuss the use of insulin produced by genetically modified bacteria, and the potential use of stem cells, to treat diabetes mellitus (HSW6a, 7b); Insulin made by genetically modified bacteria, when compared with insulin derived from pigs and cattle, is: cheaper to produce with a more rapid response less chance of an immune reaction effective in people whove built up a tolerance to animal derived insulin has fewer ethical issues (ie. for vegetarians) less risk of cross species infection

(i) outline the hormonal and nervous mechanisms involved in the control of heart rate in humans.

4.2.1 Excretion Context and exemplification Assessable learning outcomes The kidneys, liver and lungs are all involved in the removal of toxic products of metabolism

21 from the blood. The liver also metabolises toxins that have been ingested. The kidneys also play a major role in the control of the water potential of the blood.

Candidates should be able to: (a) define the term excretion;

(b) explain the importance of removing metabolic wastes, including carbon dioxide and nitrogenous waste, from the body; Excess carbon dioxide dissolves in the water in the blood to produce carbonic acid, this lowers pH of the blood causing respiratory acidosis which can cause breathing difficulties, headaches and drowsiness. Carbon dioxide can bind with haemoglobin to form carbaminohaemoglobin which has a low affinity for oxygen meaning oxygen is less efficiently transported. Also carbon dioxide forms hydrogen carbonate ions which compete with oxygen for space on the haemoglobin, reducing oxygen transport. The amino group on amino acids can be very toxic but proteins and amino acids are very high in energy so it would be wasteful to remove them from the body as they are, so the amino group can be removed to form ammonia and a keto acid using oxygen which is deamination. The ammonia is then turned into urea in the ornithine cycle. The keto acids can be respired. (c) describe, with the aid of diagrams and photographs, the histology and gross structure of the liver;

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The bile canaliculi are where bile is secreted and then carried to the bile ductile then carried to the bile duct then carried to the gall bladder then to the small intestine. The hepatic artery carries oxygenated blood to the liver, the hepatic portal vein brings blood from the small intestines, and this means that any harmful substances ingested will be broken down quickly by the liver cells. There are

23 branches of the hepatic artery, hepatic portal vein and bile duct to each liver lobule, the hepatic artery and hepatic portal vein both link to the central vein via the sinusoids.

(d) describe the formation of urea in the liver, including an outline of the ornithine cycle; Amino acids are deaminated with oxygen in the hepatocytes. Amino acid + Oxygen Keto acid + Ammonia The keto acid is then either respired or stored. Keto acids are respired in this way:

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The ammonia is turned into urea in the ornithine cycle. Ammonia + Carbon dioxide Urea + Water 2NH3+CO2CO(NH2)2+H2O The ornithine cycle looks like this:

(e) describe the roles of the liver in detoxification;

25 The liver detoxifies various substances in the blood, such as alcohol, paracetamol, hormones and hydrogen peroxide. It can catalyse the breakdown of 5 million molecules of H2O2 to harmless substances in a minute. It breaks down alcohol, into ethanoate (aka acetate) which can be respired when it can join with Coenzyme A to form acetyl Conenzyme A. Ethanol ---(alcohol dehydrogenase)(oxidised NAD reduced NAD)--->Ethanal (this occurs in the cytosol) Ethanal---(aldehyde dehydrogenase)(oxidised NAD reduced NAD)-->Ethanoate (this occurs in the mitochondria) The ethanoate enters the Krebs cycle, where it can be respired. If a person drinks too much alcohol this can lead to liver cirrhosis:

(f) describe, with the aid of diagrams and photographs, the histology and gross structure of the kidney;

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28 (g) describe, with the aid of diagrams and photographs, the detailed structure of a nephron and its associated blood vessels;

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Glomurelar filtrate

(h) describe and explain the production of urine, with reference to the processes of ultrafiltration and selective reabsorption; Ultrafiltration

Blood flows into the glomerulus via the afferent arteriole which is at a higher pressure than the blood that leaves through the efferent arteriole because of the difference in the diameters of the lumens of these vessels. The blood in the glomerulus is under very high pressure and must pass through three different layers in order to enter the Bowmans capsule: Endothelium of capillaries- contains gaps through which blood plasma passes as well as the substances dissolved in it.

30 Basement membrane (which the feet of the podocytes adhere to)- a fine mesh of collagen fibres and glycoproteins that do not allow molecules with an Mr larger than 65000-69000 to pass through (usually proteins). Epithelium of the Bowmans capsule- podocytes of the renal cell have the fingerlike protrusions very close together and the filtrate passes between them.

This forms the glomurular filtrate from the blood. Selective Reabsorbtion: Na+ ions are actively transported out of the wall of the proximal convoluted tubule and enter the surrounding tissue fluid. This creates a low [Na + ions] in the cells of the epithelium of the tubule. This creates a concentration gradient into the epithelium from the lumen, Na+ pass into these cells and as these go into the cells they cotransport amino acids and glucose into the epithelial cells as the concentrations of amino acids and glucose in the cells rise they diffuse into the tissue fluid, then diffuse into the blood and are carried away. Useful solutes such as glucose, amino acids, vitamins and some salts are reabsorbed by active transport and facilitated diffusion. The structure of the tubules can help with this: Microvilli increase surface area It has cotransporter proteins for amino acids and glucose. It has Na/K pumps to actively transport the ions against the concentration gradient. It has many mitochondria to produce ATP by aerobic respiration for the active transporter proteins.

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Countercurrent multiplier effect of the loops of Henle

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The loop of Henle acts operates a countercurrent multiplier effect. Countercurrent refers to the opposing flow of filtrate in the ascending and descending limbs. It is easiest to explain in reverse. Near the top of the ascending limb Na+ and Cl- ions are actively pumped out of the filtrate, into the tissue fluid of the medulla. The ascending limb is impermeable to water so the water stays inside the tubule. This creates a low water potential in the tissue fluid of the medulla, because theres a high concentration of ions there. Because theres a lower water potential in the tissue fluid this creates a water potential gradient between the filtrate in the descending limb of the loop of Henle and the tissue fluid, and because the epithelium making up the walls of the tubule of the descending limb are permeable to water this allows water to leave the filtrate into the tissue fluid by osmosis. The descending limb is impermeable to ions and this prevents the ions from reentering the filtrate, and means that the water must leave to redress the water potential gradient. Also the counter-current multiplier effect maintains a steep water potential gradient all the way along the descending limb. This happens because at the start of the ascending limb there is a very high concentration of ions so many of these ions are actively transported out leading to a very low water potential in the tissue fluid, so a water potential is maintained with the filtrate in the descending limb even though lots of water has left the descending limb already. As well as this the collecting duct passes through the medulla and has a good deal of water leave it by osmosis because of the low water potential of the tissue fluid of the medulla, further aiding the reabsorption of water. (i) explain, using water potential terminology, the control of the water content of the blood, with reference to the roles of the kidney, osmoreceptors in the hypothalamus and the posterior pituitary gland;

33 Osmoreceptors in hypothalamus in the brain detect the low water potential of the blood flowing through it and so produce more ADH which passes down the axons of the cells into the posterior piturity gland to be secreted (neurosecretion) into the blood. The blood takes the ADH to the kidneys where it binds to the receptors on the cell surface membranes of the cells lining the collecting ducts. This triggers a sequence of enzyme controlled reactions leading to the production of an active phosphorylase enzyme which triggers vesicles with aquaporins in the surface to move towards the plasma membrane, so the lining of the collecting duct becomes more permeable to water so water can flow out of the urine so more is reabsorbed into the blood so the water potential of the blood goes up. Osmoreceptors in the hypothalamus detect the high water potential and secrete less ADH so less passes down the axons, so less is neurosecreted into the blood from the posterior piturity gland so less reaches the collecting ducts so less binds with the receptors on the collecting ducts so aquaporins move out of the plasma membranes of the cells the epithelium of the collecting duct is less permeable so less water leaves the urine so less water is reabsorbed in the blood so the water potential of the blood goes down.

(j) outline the problems that arise from kidney failure and discuss the use of renal dialysis and transplants for the treatment of kidney failure (HSW6a, 6b, 7c); Kidney failure means that the blood is not filtered, so urea can build up to dangerous levels. Also excess ions cannot be removed from the blood and the osmotic potential of the blood cannot be managed and so this can be fatal.

34 Dialysis can be used to replace the kidneys in a temporary way. There are two types: Haemodialysis- The substances in the dialysis fluid are at the same concentrations as the normal level in blood plasma and it is kept constantly flowing over blood within the partially permeable membrane so that the excess ions and urea leave by diffusion and the water potential becomes normal by osmosis. Peritoneal Dialysis- The peritoneum is the layer of tissue that lines the abdominal cavity. In peritoneal dialysis a catheter is inserted into the peritoneal cavity and dialysis fluid is passed into the cavity and is left there for a hour, it takes up wastes from the blood and can be drained off again later. This is less efficient than haemodialysis but it frees the patient from being connected to machine during the procedure but it does have to be done more often, but peritoneal dialysis is a continuous process so there shouldnt be so big swings in blood volume or content. Transplants are possible to avoid the need for regular dialysis. Transplants need a close match to reduce the risk of rejection and reduce the need for immunesuppressant drugs. However there is a limited supply of transplant organs. Xenotransplantation is possible, but there are ethical issues, as well as the possibility of introducing viruses from animals to humans.

(k) describe how urine samples can be used to

35 test for pregnancy and detect misuse of anabolic steroids (HSW6a, 6b).

Anabolic steroids are drugs that build up muscle tissue. Anabolic steroid hormones stimulate anabolic reactions in body cells- reactions where larger molecules are built up from smaller ones. They are banned in some sports to try and stop the misuse of some steroids that can have negative side effects such as liver damage. It is also considered unfair on some athletes. Steroids are naturally removed from the blood in the urine so athletes can have their urine regularly tested for steroids. This testing for steroids (or the breakdown products of steroids) is done using Gas Chromatography. The sample is vapoourised and passed through the column and the time taken for each substance to pass through the column is timed and compared to the time it takes known samples of steroids to pass through. If the times are the same then the sample contains the steroid.

4.3.1 Photosynthesis Context and exemplification Assessable learning outcomes Photosynthesis is the process whereby light energy from the Sun is transformed into chemical energy and used to synthesise large organic molecules from inorganic substances. Photosynthesis forms the basis of most food chains. Candidates should be able to: (a) define the terms autotroph and heterotroph;

36 Autotroph- An organism that makes its own organic nutrients using an inorganic carbon source. Heterotroph- An organism that requires organic nutrients from other organisms to supply it with a source of carbon. (b) state that light energy is used during photosynthesis to produce complex organic molecules; Light energy is used during photosynthesis to produce complex organic molecules. (c) explain how respiration in plants and animals depends upon the products of photosynthesis; Photoautotrophs and heterotrophs can release the chemical potential energy in complex organic molecules which were made during photosynthesis- respiration. They use oxygen, which was first released into the atmosphere as a product of photosynthesis, for aerobic respiration. (d) state that in plants photosynthesis is a twostage process taking place in chloroplasts; In plants, photosynthesis is a two-stage process taking place in chloroplasts. (e) explain, with the aid of diagrams and electron micrographs, how the structure of chloroplasts enables them to carry out their functions; The chloroplast envelope surrounds it, it has more membranes inside the chloroplast. These membranes are called thyladkoids and the fluid filled sacs are called thylakoids. In parts these thylakoids are stacked up into grana. The background material inside the chloroplast is called the stroma. Embedded in the thylakoid membranes are photosystems made up of photosynthetic pigments. Also embedded in these membranes are electron carriers. These membranes have a large surface area, to give lots of space for the photosynthetic pigments, electron carriers and ATP synthase, all involved in the light-dependent reaction. The stroma contains the enzymes needed to catalyse the reactions in the lightindependent stage. Chloroplasts can make some of the proteins they need for photosynthesis using the genetic instructions on their chloroplast DNA, and the chloroplast ribosomes to assemble the proteins.

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(f) define the term photosynthetic pigment; Photosynthetic pigment-a molecule that absorbs specific wavelengths of light, and transfers the light energy to chemical energy. (g) explain the importance of photosynthetic pigments in photosynthesis; The photosynthetic pigments are arranged in clusters called photosystems in the thylakoid membranes. There are accessory pigments such as chlorophyll b and carotene which absorb the light energy and pass it on to the molecules of chlorophyll a (primary pigment) in the reaction centre of the photosystem. The chlorophyll a releases a high energy electron into the electron transport chain. These electrons are very important as they can pass through the electron transport chain, and they are replaced by electrons released from the photolysis of water.

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(h) state that the light-dependent stage takes place in thylakoid membranes and that the light-independent stage takes place in the stroma; The light-dependent stage takes place in thylakoid membranes and that the light-independent stage takes place in the stroma. (i) outline how light energy is converted to chemical energy (ATP and reduced NADP) in the light-dependent stage (reference should be made to cyclic and non-cyclic photophosphorylation, but no biochemical detail is required); A photon of light energy hits an accessory pigment (eg. chlorophyll b) and the energy is absorbed and passed from molecule to molecule until it reaches the reaction centre of the photosystem to a primary pigment (eg. chlorophyll a (or the photon can just hit the primary pigment direct)). This energy is transferred to a pair of electrons and they become excited. These electrons pass through the electron transport chain, through a series of electron carriers. Energy is released as the electrons pass down these electron carriers and this energy is used to pump protons across the thylakoid membranes into the thylakoid space, these protons then flow down the proton gradient through ATP synthase molecule, this chemiosmosis forms ATP from ADP and Pi. This ATP is used in the lightindependent stage of photosynthesis. The making of ATP using light energy is called photophosphorylation. There are two types of photophosphorylation: cyclic and non-cyclic. These can be represented in Z-scheme.

39 Non-cylcic: In non-cyclic photophosphorylation, the electrons leave photosystem II (P680) and are replaced by electrons released from the photolysis of water (2H 2O4H+ +4e-+O2). These electrons pass on through the electron carriers to the photosystem I (P700) where they are excited again by light and they pass through an electron transport chain again and join with oxidised NADP, H + to form reduced NADP, rather than returning to the PSII. This reduced NADP goes to the Calvin cycle and is used, along with the ATP produced in the light dependent stage, to form TP from GP in the Calvin cycle.

Cyclic phosphorylation: This one only involves photosystem I and in cyclic phosphorylation the electrons released from the exciting photosynthetic pigments return to the photosystem

40 again after passing through the electron transport chain, producing ATP in the process.

(j) explain the role of water in the light dependent stage; The electrons lost from chlorophyll a in photosystem II are replaced by the photolysis of water. Like this : 2H2O4H++4e-+O2 (k) outline how the products of the light dependent stage are used in the light independent stage (Calvin cycle) to produce triose phosphate (TP) (reference should be made to ribulose bisphosphate (RuBP), ribulose bisphosphate carboxylase (rubisco) and glycerate 3-phosphate (GP), but no other biochemical detail is required); The products of the light dependent stage are ATP, reduced NADP and oxygen. The ATP and reduced NADP are used in the Calvin cycle, like this:

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(l) explain the role of carbon dioxide in the light-independent stage (Calvin cycle);

(m) state that TP can be used to make carbohydrates, lipids and amino acids; TP can be used to make carbohydrates, lipids and amino acids. (n) state that most TP is recycled to RuBP; Most TP is recycled to RuBP, in fact 10 out of 12 molecules of triose phosphate are used to regenerate RuBP (ribulose bisphosphate). (o) describe the effect on the rate of photosynthesis, and on levels of GP, RuBP and TP, of changing carbon dioxide concentration, light intensity and temperature;

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Light Intensity: Low light intensity means that the products of the light dependent stage (reduced NADP and ATP) will be in short supply so this means that the conversion of GP to TP will be slow and therefore the levels of GP will rise (as its still being made) and levels of TP and RuBP will fall as they arent being produced as fast but are still being turned into GP.

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Temperature: All the reactions in the Calvin cycle are catalysed by enzymes. At low temperature all the reactions will be slower as the enzymes work more slowly. This means the levels of RuBP, GP and TP will fall. At high temperatures the enzymes will denature and so levels of GP, TP and RuBP will reduce. Not only this, at higher temperatures rubisco becomes less specific and starts catalysing photorespiration in which it combines oxygen with RuBP, wasting RuBP and reducing the efficacy of photosynthesis at higher temperatures.

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Carbon dioxide: At low CO2 concentrations, the fixing of CO2 is slow as not much collides with rubisco enzymes and so conversion of RuBP to GP is also slow as theres less CO 2 to combine with the RuBP to produce GP. So the level of RuBP will rise because its still being produced and levels of GP and TP will fall because they are being used to make RuBP. (p) discuss limiting factors in photosynthesis with reference to carbon dioxide concentration, light intensity and temperature; There is only one limiting factor at a time.

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(q) describe how to investigate experimentally the factors that affect the rate of photosynthesis (HSW3) Could measure: Volume of O produced Rate of uptake of CO Rate of increase in dry mass of plants The factors that affect the rate of photosynthesis can be investigated using Canadian pondweed. A test tube containing the pondweed and water is connected to a capillary tube full of water. The tube of water is connected to a syringe. A source of white light is placed at a specific distance from the pondweed and the weed is left to photosynthesise for a set period of time. As it photosynthesises the oxygen released will collect in the capillary tube. At the end of the test period the syringe can be used to move the oxygen bubble to the ruler and measure the length of the oxygen bubble to determine the volume of O2. Any variables that could affect the results should be control other than the

48 one you want to test. Repeat the experiment and calculate a mean. Then repeat the whole thing with either the lamp further or closer to the pondweed to investigate light intensity, or put the tube in a temperature controlled water bath, or use sodium hydrogen carbonate to add CO 2 to the water.

Module 4: Respiration

Respiration is one of the fundamental biological processes and takes place in all living things. Most definitions of life have respiration as a necessary criterion.

Links

GCSE Criteria for Science: 3.7(i) (a); 3.9(i) (b)

From other modules within this specification:

F211 Module 1; F212 Module 2.

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4.4.1 Respiration

Context and exemplification

Assessable learning outcomes

Respiration is the process whereby energy stored in complex organic molecules is transferred to ATP.

ATP provides the immediate source of energy for biological processes.

Candidates should be able to:

(a) outline why plants, animals and microorganisms need to respire, with reference to active transport and metabolic reactions;

Organisms need to respire in order to produce ATP which can be used in active transport and in metabolic reactions. (b) describe, with the aid of diagrams, the structure of ATP;

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(c) state that ATP provides the immediate source of energy for biological processes;

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(d) explain the importance of coenzymes in respiration, with reference to NAD and coenzyme A;

Oxidised NAD can be reduced to reduced NAD when it accepts a hydrogen, and it can remove these hydrogens during glycolysis to allow the production of pyruvate. These hydrogens can either be accepted in the anaerobic pathway (by ethanal in yeast which then becomes ethanol, or by pyruvate in mammals to produce lactate), or these hydrogens can carry electrons to the electron transport chain (and also hydrogen ions which are then actively transported into the intermembranal space. Lots of diagrams below to illustrate

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(e)

state that glycolysis takes place in the cytoplasm;

Glycolysis takes place in the cytoplasm. (f) outline the process of glycolysis beginning with the phosphorylation of glucose to hexose bisphosphate, splitting of hexose bisphosphate into two triose

53 phosphate molecules and further oxidation to pyruvate, producing a small yield of ATP and reduced NAD;

Net gain of 2 ATP and 2 reduced NAD. Glycolysis begins with the phosphorylation of glucose to hexose bisphosphate using 2 molecules of ATP. Hexose bisphosphate splits into 2 triose phosphate molecules. The 2 triose phosphates then are further oxidised to 2 pyruvate molecules, reducing 2 NAD coeznymes and turning 4 ADP into 4 ATP in the process. (g) state that, during aerobic respiration in animals, pyruvate is actively transported into mitochondria; During aerobic respiration in animals pyruvate is actively transported into the mitochondria to do the link reaction. (h) explain, with the aid of diagrams and electron micrographs, how the structure of mitochondria enables them to carry out their functions;

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The cristae give a large surface area to put many electron transport chains and oxysomes for ATP synthesis. There are many oxysomes with ATP synthase to produce ATP from ADP+Pi. The inner mitochondrial membrane is impermeable to most small ions, including protons to ensure that the proteins dont leak through the membrane and to make sure they pass through ATP synthase producing ATP rather than just diffusing through the membrane. The electron transport chains can use the energy from the electrons passing through them to pump H+ ions into the intermembranal space. In the matrix: (i) Lots of enzymes to catalyse the different stages of aerobic respiration. There are lots of molecules of oxaloacetate to reaction with the acetate coming in from the link reaction. Lots of molecules of NAD Mitochondrial DNA that codes to form mitochondrial enzymes. Mitochondrial ribosomes can be used to produce those enzymes and proteins. state that the link reaction takes place in the mitochondrial matrix;

The link reaction occurs in the mitochondrial matrix. (j) outline the link reaction, with reference to decarboxylation of pyruvate to acetate and the reduction of NAD;

56 2x pyruvate (3C) -----(2x oxidised NAD 2x reduced NAD [Pyruvate dehydrogenase])----(2CO2 [Pyruvate decarboxylase])----> 2x acetate (2C) 2x acetate (2C) -----(Coenzyme A)-------> 2x acetyl coenzyme Overall produces 2 reduced NAD, 2 CO2 and 2 acetyl CoA (k) explain that acetate is combined with coenzyme A to be carried to the next stage; CoA is a coenzyme that carries the acetate to the next stage, and this the purpose of the link reaction. (l) state that the Krebs cycle takes place in the mitochondrial matrix; The Krebs cycle occurs in the mitochondrial matrix. (m) outline the Krebs cycle, with reference to the formation of citrate from acetate and oxaloacetate and the reconversion of citrate to oxaloacetate (names of intermediate compounds are not required);

57 Acetyl CoA drops off the acetyl group (2C) on the oxaloacetate (4C), this forms citrate. A carbon dioxide leaves the citrate forming a 5C intermediate. Then an oxidised NAD forms a reduced NAD and a CO2 leaves as well, forming a 4C intermediate. This 4C intermediate phosphorylates an ADP+P i into an ATP and reduces 2 oxidised NAD molecules into 2 reduced NAD molecules and reduces an oxidised FAD molecule to a reduced FAD molecule. The oxaloacetate is regenerated to be used in the Krebs cycle again.

(n) explain that during the Krebs cycle, decarboxylation and dehydrogenation occur, NAD and FAD are reduced and substrate level phosphorylation occurs; Acetyl CoA drops off the acetyl group (2C) on the oxaloacetate (4C), this forms citrate. A carbon dioxide leaves the citrate forming a 5C intermediate, this is called decarboxylation. Then an oxidised NAD forms a reduced NAD and a CO 2 leaves as well (decarboxylation), forming a 4C intermediate. This 4C intermediate phosphorylates an ADP+Pi into an ATP (substrate level

58 phosphorylation) and reduces 2 oxidised NAD molecules into 2 reduced NAD molecules and reduces an oxidised FAD molecule to a reduced FAD molecule. (o) outline the process of oxidative phosphorylation, with reference to the roles of electron carriers, oxygen and the mitochondrial cristae;

Oxidative phosphorylation is the formation of ATP by the addition of an inorganic phosphate to ADP in the presence of oxygen. The coenzymes reduced NAD and reduced FAD carry Hydrogen atoms to the electron transport chain. These form H+ atoms and electrons. The electrons pass down the electron transport chain, through three electron carriers of decreasing energy level, loosing energy at each carrier. This energy level is used by the electron carriers to pump the H+ ions into the intermembrane space. The concentration of protons inside the intermembrane space is now higher than the concentration outside so there is now an electrochemical gradient and the protons flow back into the mitochondrial matrix through oxysomes through molecules of ATP synthase, producing ATP by chemiosmosis. At the end of the electron transport chain the electrons are accepted by the final electron acceptor, O2 and combine with H+ ions too to form water. The cristae are folded to give a large surface area for oxysomes and electron transport chains to be on. (p) outline the process of chemiosmosis, with reference to the electron transport chain, proton gradients and ATPsynthase (HSW7a); The energy from the electron transport chain is used to pump protons into the intermembrane space which diffuse down the concentration gradient into the mitochondrial matrix through oxysomes, thorugh ATP synthase producing ATP,

59 because it cannot diffuse through the lipid part of the membrane. This flow of hydrogen ions is called chemiosmosis. (q) state that oxygen is the final electron acceptor in aerobic respiration; Oxygen is the final electron acceptor in aerobic respiration, accepting electrons and combining with H+ ions to form water. O2+4H++4e-2H2O (r) evaluate the experimental evidence for the theory of chemiosmosis (HSW1); The pH of the intermembrane space in mitochondria was found to be lower than the pH of the matrix, therefore there is a proton gradient between the intermembrane space and the matrix of the mitochondria. Artificial vesicles were created from phospholipid bilayers to represent the inner mitochondrial membrane, with light activated proton pumps and ATP synthase molecules. When the proton pump is active, the ATP synthase produces ATP, showing it is possible to produce ATP this way, although not neccassarily that this is how it is done in mitochondria. Uncouplers, such as 2,4-dinitrophenol destroy the proton gradient across the inner mitochondrial membrane and when uncouplers are added to mitochondria no ATP is made. Mitochondria placed in a solution at pH 8 until the whole mitochondrion (intermembrane space and matrix) was at pH 8. When ADP and P i was added no ATP was produced by these mitochondria. These mitochondria were transferred to a more acidic solution of pH 4, the outer membrane of the mitochondrion is permeable to protons, the protons moved into the intermembrane space, creating a proton gradient across the inner mitochondrial membrane, and in the presence of ADP and Pi ATP was produced. (s) explain why the theoretical maximum yield of ATP per molecule of glucose is rarely, if ever, achieved in aerobic respiration; It is not achieved because some ATP has to be used to actively transport the pyruvate into the mitochondrion from the cytoplasm. Also there is not 100% efficiency because some protons leak through the lipid part of the membrane, rather than through the ATP synthase, therefore not producing all the possible ATP. (t) explain why anaerobic respiration produces a much lower yield of ATP than aerobic respiration; Anaerobic respiration allows glycolysis to continue but without oxygen to act as the final electron acceptor the electron transport chain cannot continue, so oxidative phosphorylation cant work, so the link reaction wont continue so the only ATP produced is produced by glycolysis, which isnt very much so it has a

60 very low yield of ATP as the most productive parts of respiration cant continue, only glycolysis. (u) compare and contrast anaerobic respiration in mammals and in yeast;

In mammals

In fungi and plants In mammals pyruvate accepts a hydrogen from reduced NAD forming lactate and oxidised NAD, involving the enzyme lactate dehydrogenase.

61 In fungi and plants ethanal is formed by the decarboxylation of pyruvate releasing CO2 by the action of the enzyme ethanal dehydrogenase. The ethanal accepts a hydrogen from reduced NAD and forms ethanol by the action of ethanol dehydrogenase forming ethanol and oxidised NAD. Either way the oxidised NAD can be used to pick up a hydrogen from triose phosphate and allows glycolysis to continue. (v) define the term respiratory substrate;

(w) explain the difference in relative energy values of carbohydrate, lipid and protein respiratory substrates. Carbohydrates and proteins have similar energy values (releasing about 17 kJ/g), whereas the values for fats are much higher (around 39 kJ/). The reason for the greater energy value is mainly due to the higher proportion of H atoms compared with C and O atoms in fat molecules, this is because of the long chains of carbon and hydrogen, the fatty acids.

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Practical Skills (HSW5) are assessed using specific OCR-set experiments. The practical work outlined below may be carried out as part of skill development.

Collection of quantitative data:

Investigate the effect of a variable on the rate of respiration of an animal or microorganism;

Compare aerobic and anaerobic respiration in yeast.

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Presentation, analysis and evaluation of quantitative data:

Calculate rates of respiration;

Plot graphs showing the effect of a variable on the rate of respiration. Evaluation of data collection strategies: Identify and evaluate the limitations of measuring rates of respiration.