Biology F214

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  • Created on: 03-06-15 08:53

Communication and Homeostasis

Organisms need to respond to external stimuli. e.g. temp, oxygen, level of sunlight

These can occur over time, e.g. winter to summer fur

Or they can occur quickly, e.g. change of pupil size

Internal enviroments also change, e.g. conc. of CO2

Good communication involves:

Covering the whole body

Enables cells to communicate with each other

Enables specific communication

Enables rapid communication

Enable both short and long term repsonses

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Cell Signalling

Cells need to communicate with each other by a process called cell signalling

Cell Signalling can be Hormonal or Neuronal

Negative feedback:

A process in which any change in a parameter brings about a reversal of that change so that the parameter is kept fairly constant

Positive Feedback:

A process in which any change in a parameter brings about an increase in change in that change


The maintenance of a constant internal enviroment despite external changes

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Physiological and Behavioural responses to change

Ectotherms- Cold blooded, rely on the sun to keep their core temp stable

Endotherms- Hot blooded, uses functions of the body such as respiration and sweating to keep a constant core temp.


Physiological- The horned lizard expands its ribcage and the frilled lizard uses its frill to expand its surface to absorb more heat from the sun. Locus increase their abdominal breathing movements to increase water loss when hot

Behavioural- Snakes expose their body to the sun so more heat is absorbed. Locusts orientate their body towards the sun to expose a large surface area and more so more heat is absorbed, by orienating away from the sun, more heat is lost. Lizards hide in burrows to prevent heat absorption by staying out of the sun.

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Physiological and Behavioural responses to change



Sweat Glands, when hot they secrete sweat onto the skin. Water evaporates using heat from the blood to supply latent heat of evaporisation. When cold, less sweat is secreted, less water is evaporated and so less loss of latent heat.

Lung, Nose and Mouth, When hot, panting increases water evapor from lungs, tongue and moist surfaces. Loss of latent heat as above. When cold, no panting, less water evap, so less loss of latent heat.

Hair on skin, When hot, the hairs lie flat, providing little insultation, meaning heat can be lost through convectionand radiation. When cold, hairs raise to trap a layer of air, insultating the skin and reducing heat loss.

Arterioles leading to capillaries in skin, Hot- vasodilation allows more blood to capillaries near skin surface, so heat can radiated from the skin. Cold- Vasoconstriction reduced the flow of blood through the capilaries near the skin , so less heat is radiated.

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Physiological and Behavioural responses to change

Liver cells, Hot- reduce rate of meatabolism so less heat is generated from exergonic reaction e.g. repsiration. Cold- increases rate of metabolism so more heat is generated. Respiration generates more heat which is transfered to the blood.

Skeleteal Muscles, Hot- not spontantious contarction. Cold- Spontaneous contraction generates heat as muscle cells repsire.


Hot- Move into shade or hide in burrow. Orientate body to decrease surface area exposed to the sun. Remain inactive and spread out limbs to increase surface area

Cold- Move into sunlight, oreinatate body to increase surface area exposed to sun. Move about to generate heat in muscles. Rolling into a ball to decrease surfaec area.

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Endotherms moniter blood temp in the the hypothalamus. If the core temp drops or rises it sends signals to the effector to reverse this change.

Peripheral temp. receptors moiter the extremities. The information is fed to the thermoregualatory centre. If it signals a temp. change to the brain, it can initate behaviour mechanisms for mainatining body temp.

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Sensory receptors to nerve impulses

Light sensitive cells in the retina detect light intensity and ranges of wavelength (colour).

Olfactory cells in the naval cavity detect the presense of volatile chemicals.

Tastebuds detect the presense of soluble molecules

Pressure receptors in the skin detect pressure on the skin.

Sound receptors in the cochlea detect vibrations inn the air.

Muscles spindles detect the length of muscle fibres

These are all tranductors and convert stimuli to a action potential. 

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Motor neurones

A cell body at the end with a large nucleus and lots of rough ER and golgi bodies

Many short dendrites that carry nerve impulses to the cell body

An long axin which carries an impulse from the cell body to the effector.(

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Sensor Neurone

Long processes on eithr side of the cell body

A dendron carring nerve impulses from a receptor to the cell body

An axon carrying an impulse from a receptor to the central nervous system


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Action Potentials

The resting potential is maintained and established by sodium potassium pumps

When not conducting a action potential, the potnetial difference acroos the membrane is -60mV.

Sodium potassium pumps actively transport 3 Na + ions out for every 2 K+ ions in.

The axon contains organic anionsm which the membrane is impermeable to.

Slight loss of K+ ion through permeable membrane.

Membrane permeable to Na + ions.

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How an action potential is generated

The membrane is at a resting state; -60mV inside compared to outside. Polarised

Na+ ion channels 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 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 Na+ ion channels shut and the K+ ion channels open.

K+ ions diffuse out of the cell, bring the potential difference back to negative compared with the outside, Repolarised

The potential difference overshoots slightly, making the cell hyperpolarised

The original potential difference is restored, so the cell returns to its resting state.

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Action potential in a myelinated neurone

The myelinated sheath is an insultating layer of aftty material which Na and K ions cannot pass through. Between the schwann cells are gaps, node of Ranvier, which contain Voltage- gated Sodium and Potassium ion channels, allowing ionic exchnage to occur. The action potential 'jumps' from one node to the other, Saltatory conduction.


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The significance of the Frequency of AP

-A stimulus at the higher intensity will cause the sensory neurones to produce more generator potentials.

-More frequent action potentials in the sensory neurone

-More vesicles realeased at the synapse

-Higher frequency of action potentials in the postsynaptic neurone

-A higher frequency of signals to the brain

-A more intense stimulus

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Myelinted vs. Non-myelinated


100-120 m/s (Fast response time)

Up to 1m transmission distance

Used in movement

1/3 of all neurones

One neurone is surrounded by one shwann cell, wrapped round many times


2-2- m/s (Slow response time)

mm or cm transmission distance

Used in bretahing and respiation

Many nerounes surrounded by one schwann cell.

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Structure of Synapse

Synaptic knob: Many mitochondria, A large amount of smooth ER, Vesicles contain acetylcholine, Voltage gated sodium ion channels in the membrane

Posynaptic membrane: Specialised ligand sodium ion channels that will only open when acetylcholine binds to them.

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The role of neurotransmitters in action potentials

A neurotransmitter is a chemical that diffuses across the cleft of the synapse to transmit a signal to the postsynaptic neurone. They cause the generation of a new action potential in the postsynaptic neurone. In cholinergic synapses the neurotransmitter is acetylcholine. It is stored in vesicles in the synaptic knob, and when the action potential arrives, the voltage gated sodium ion channels open, so calcium ions diffuse out. This causes the vesicles to fuse with the synaptic membrane, so acetylcholine is released by exocytosis. It diffuses across the cleft and binds to receptor sites on the sodium ion channels on the postsynaptic membrane. Sodium ions diffuse across the synaptic membrane into the postsynaptic neurone, creating a generator potential. If the generator potential is sufficient, the potential across the membrane reaches the threshold potential, and a new action potential is created. 

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Role of Synapses

The role of a synapse is to connnect two neurones togethere to pass on a signal.

-Several presynaptic neurones can converge from differnet parts of the body to create the same reponse.

-One pr-synapse can diverge to several po-synapses, to allow one impulse to transmit to several parts.

-They ensure that signals are tranmitted in one direction- only pre-synaptic knob has ACh

-Filter out unwanted low-level signal. Several vesciles need to be released to pass on a AP

-Low level signals amplified by summation

- Acclimatisation, after repeated stimulation, as synapse may run out of vescicles of ACh. The synapse is fatigued. This avoids overstimulation which can damage effectors.

-The specific pathway in the nervous system is thought to be the basis of conscious though and memory.

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Endocrine, exocrine and target tissue

Endocrine Glands: a gland that secrets hormones directly into the blood. Endocrine glands have no ducts.

Exocrine Glands: a gland that secretes molecules sirectly into a duct that carries molecules to where they are used.

Hormones; A molecules released into the blood which acts as a chemical messenger

Target tissue: a group of cells that have receptors embedded in the plasma membrane that are complementary in shape to specific hormone molecules. Only these cells will repsond to the specific hormones.

First messenger and Secondary Messenger

The first messenger is the hormone that transmits a message around the body, e.g. adreanline.

The secondary messenger, e.g. cAMP transmits a signal inside the cell

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Function of the adrenal glands

The adrenal galnd has two regions: cortex and medulla region


Relaxes smooth muscle in the bronchioles 

Increases the stroke volume of the heart

Increases heart rate

Causes general vasoconstriction- raising blood pressure

Stimultates conversion of glycogen to glucose

Dilates pupils

Increases mental awareness

Inhibits action of the gut

Cuses body hair erect

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Function of the adrenal glands


Mineralalocorticoids help control the concentration of Na and K in the blood

Glucocortoids help control the metabolism of carbohydrates and proteins in the liver

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Histology of pancreas

The cell surrounding excorine gland of the pancreas secretes digestive enzymes into the pancreatic duct, which then goes onto the small intestine. This is the majority of the pancreas.

The exocrine cells- the islets of Langherhans- consists of a and B cells. The a cells manufacture and secrete glucagon, whereas the B cell manufacture and secrete insulin. They are involved in the regulation of blood gkucose levels.


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Blood glucose Concentration (Low)

If blood glucose conce gets too low:

Detected by a cells

The fall inhibits insulin production production

They secrete glucagon into the blood

Bind to receptors on hepatocytes

-Glycogenolysis- conversion of glycogen to glucose

-More fatty acids are used in respiration 

-Gluconeogenesis- covenversion of amino acids and fats to glucose

More glucose in the bloodstream

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Blood glucose Concentration (High)

Detected by B cells

The rise inhinits glucagon production

Secrete insulin into blood

Bind to receptors on hepatocytes, in the liver

This activates adenyl cyclase in the cell

Converts ATP to cAMP

The cAMP activates a series of enzyme catalysed reactions within the cell;

-More glucose channels are places in the cells surface membrane

-More glucose enter the cell

-Glycogenesis- glucose in the cell is converted to glycogen

-More glucose is converted to fats

-More glucose is used in respiration

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How insulin secretion is controlled

The cell membrane of the B cells contain Ca2+ and K+ ion channels

The K ion channels are normally open, and the Ca ion channels are normally shut, K ions diffuse out of the cell, making the inside more negative.

When glucose concentration outside of he cells are high, glucose molecules diffuse into the cell. 

The glucose is more quickly metabolised into ATP

The extra ATP causes the K ion channel to close.

The K ions can no longer diffuse out, so the cells become less negative inside.

The K ions can no longer diffus out, so the cells become less negative inside.

This change in potential difference opens the Ca ion channels.

Ca ions enter the cell and cause the secretion of insulin by making the vesicles contain insulin move to the cell surface membrane and fuse with it, release insulin by exocytosis.

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Diabetes Mellitus

Type 1 Diabetes:

Auto-immune disease in which body's B cells are attacked and so insulin is not produced.

Treatment- injection and blood glucose concentration are closely monitered

Type 2 Diabetes:

Body can produce insulin but insulin receptors lose ability toe detect and respond to insulin

Treatment- monitering and controlling diet and may be supplemented by injections.

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Insulin production

GM bacteria:

Exact copy of human insulin.

-Faster acting

-More effective

Less chance of developing tolerance

Less chance of rejection


More adaptable to demand

Less likely to have moral objectifications

Stem Cells:

Could be used to produce new B cells

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Hormonal and nervous mechanism of heart rate

AP sent down the accelerator nerve to the heart; from the cardiovascular centre of the medulla oblongata cause the heart to speed up. This may be because of:

-Movement of limb detected by stretch receptors in muscles, extra oxygen needed.

Drop in pH detected by chemoreceptors in the carotid arteries, the aorta and the brain (when we exercise we produce CO2, this reacts with H2O in the blood and reduce the pH).

-CO2+ H2o--> H2CO3

-H2CO3--> H+ + HCO3

Action potential sent down the vagus nerve decreases the heart rate. This may be because of:

-Blood pressure rising

When the conc. of CO2 in the blood falls, it reduces the activity of the accelerator nerve, slowing the heart rate. The presence of adranaline increases the heart rate to prepare the body for activity. 

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Excretion: The removal of metabolic wastes from the body

Importance of remving waste: Carbon dioxide must be removed as, when it dissolves in oxygen is produced hydrogencarbonate ions. These ions compete with oxygen for space on haemoglobin. Carbondioxide can also combine directly with haemoglobin, called carbaminohaemoglbin.

Can cause respiratory acidosis

Carbon dioxide dissolving in the blood plasma and combinig with water to form carbonic acid. Lowering the pH.

Nitrogen waste must be removed as the amino group is highly toxic. But proteins and amino acids are very high in energy. They are entered into the orthine cycle, the amine group is removed to form ammonia, which forms urea, water and keto acids when added to oxygen and carbon dioxide. Theketo acid is used in repsiration and the urea is transported to the kidneys for excretion.

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Histology of the Liver

The hepatic arteries supply the liver with oxgenated blood from the heart, so the liver has a good supply of oxygen for respiration, providing plenty of energy.

The hepatic vein takes deoxygenated blood away from the liver, which rejoins the vena cava and the normal circulation proceed.

Bile duct is where the subsance is secreted, which is carried to the gall bladder where it is stored until it is required in the small intestine.

The hepatic portal vein bring blood from the small intestine, the blood is rich in products from digestion, and this means that any harmful substance will be broken down quickly by the liver cells.

The liver is made of lobules, which consists of cells called hepatocytes that are arranged in rows. Each lobule has a central vein in the middle that connects to the hepatic vein. Evry single lobule has branches of the hepatic artery, hepatic portal vein and bile duct. Hepatic artery hepatic veinare connected to the central cein via capillaries called sinusoids. Hepatic artery and hepatic vein are connected to the central vein via capillaries called sinusoids. The blood flows past every hepatocyte  via the sinusoids, this ensures that the hermful stuff are broken down quickly. Also the blood provide the liver cell with oxygen. 

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Formation of Urea

Amino acid + Oxygen--> Keto acids + Ammonia

Ammonia + CarbonDioxide --> Urea + Water

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Roles of the liver in detoxification

Catalase can convert 5 million molecules of H2O2 into harmless subastance in minutes.

Alcohol contains a lot of chemical potential energy which can be used in resoiration in a minute.

Dehydrogenase catalyses the detoxification of alcohol in the hepatocytes.

Ethanol--> Ethanal --> Ethanoic Acid --> Acetyl CoA

Ethanal and ethanoic acid are dehydrogenated, and the hydrogen reduced NAD. If too many NADs are busy detoxifying alcohol, there will be to few to break down fatty acids for use in respiration, so the fatty acidsare converted into lipid, which are stored in hepatocytes, makin the liver enlarged- Fatty Liver.

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Histology and Gross Structure of Kidney

Supplied with blood from the renal artery and is drained by the renal vein. The kidney is surrounded by a tough capsule, the outer region is the cortex and the inner is the medulla. The central region if the pelvis, which leads into the ureter.


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Structure of the nephron

The nephron starts in the cortex, where the capillaries form a not called the glomerulus, surrounded by the Bowman's capsule. Fluid from the blood is pushed onto the capule by ultrafiltration. The fluid leaves the capule and flows through the nephron, starting with proximal convoluted tubule, and then into the medulla for the loop of henle, which is a hairpin counter current mulitplier. Here the compsition of the fluid is altered by selective absorbtion. Substances are reabsorbed back into the tissue fluid and capilliaries surrounding the nephron tubule. The fluid then passes into the Distal convoluted tubule, and then into the collecting duct as urine.

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Production of Urine



-Blood flows into the globerulus via the afferent arterioles which is at a higher pressure than the due to the difference in the size of the diameter of the lumen.

Blood enters the glomerulus and must pass through three distinct layers in order to enter the Bowman's capsule.

Endothelium of capillaries- contains gaps from which blood passes through as well as the substance dissolved in it.

Basement membrane- fine mesh of collagen fibres and glycoprotein that do not allow molecules with an RMM large than 69,000 to pass through (usually proteins).

Epithelium of Bowman's capsule- contain finger like projections (podocytes) that fluid from the glomerulus can pass through into the Bowman's capsule.

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Production of Urine

Selecive reabsorbtion:

Na ions are actively transported out of the wall of the convoluted tube and enter the surrounding tissue fluid

Sodium is transported into the cell with amino acids or glucose by facilitated diffusion.

As the concentration of amino acids or glucose rise they diffuse into the tissue fluid; they may also be actively removed.

They then diffuse into the blood and are carried away.

The reabsorption of salts, glucose and amino acids reduce the water potential of the cell and be rebasobed into the blood by osmosis.

Larger molecules, such as proteins, will be reabsorbed by osmosis.

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Production of Urine

Stucture of the cells of the proximal convulted tubule:

Microvilli- increase the surface area for re-absorption.

Co-transporter protein- contained in the cell surface membrane that is in contact with the tissue fluid.

Transports glucose or amino acids.

Na/K  pumps-  contained in the cellsurface membrane opposite the fluid tubule. Actively transports Na+ and K+ against their concentration gradient.

Many mitochondira- provides the energy needed to drive the selective re-absorption process. AMny mitochondria= A lot of ATP.

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Controlling water content of blood

The loop of henle, salts are transfered from the ascending limb to the descending limb. This means that tissue fluid in the medulla has a very negative water potential, as so water is lost by osmosis, particularly in the collection duct.

The water potential of the blood is monitered by osmoreceptos in the hypothalamus of the brain. When the water potental is very low, they shrink, and stimulate neurosecretory cellis in the hypothalamus. These are porduced and release anti diuretic hormones which flow down the axon to the posterior pituitary gland and where it is stored until needed. When the neurosecretory glands are stimuluated they send action potentials down their axons and cause the release of ADH. It enters the capillairies running throuugh the posterior pituitary gland. It is transported around the body and acts on the cells of the collecting ducts. When it binds to the receptors, it causes a chain of enzymes ctalysed reaction, the end result of which is the insertion of vesicles containing water-permeable channels (aquaporin) in the walls of the cells, so they are more permeable to water. More water is reabsorbed, by osmosis, into the blood. Less urine, with a lower water potential is released. Less ADH is released when the water potential rises again. The ADH is slowly broken down and the collecting ducts recieve less stimulus. 

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Problems associated with Kidney Failure


Unable to remove excess water and waste products from the body e.g. Urea and excess salts

Inability to regulate urea and salt levels



Waste, excess fluids and salts removed from the body by passing the blood over a dialysis membrane. This allows the exchange of substance between the blood and the dialysis fluid, which has the same concentration of substance as blood plasma. Subsatnce diffuse from both sides to create the correct concentration of substances.

Haemodialysis: Blood is passed through a machine that contains an artificial dialysis membrane. hepain is used to avoid clotting. Thrice weekly trips to hospitals lasting several hours.

Peritoneal: The body's own abdomenal membrane is used as a filter.

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Kidney Transplants


No dialysis

less limited diet

Better physical felling

Better quality of life

No longer 'chronically ill'


Need immunosuppressants for life of kidney

Major surgery

Risk of Infection

Need frequent checks in case of rejection

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-A human embryo secretes Human chroionic gondatropin (hGC) as soon as it is implanted on the uterine lining. The hormone can be detected in the mother's urnine after as few as 6 days.

- Pregnancy tests contain monoclonal antibodies which are tagged with a blue bead and bind only to hCG.

The hCG- antibody complex moves along the strip until it sticks to a band of immobliesd antibodies, so forms a blue line.

-One blue line is a control, so two lines indicates 

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Anabolic Steroids

Urine sample are tested using gas chromotography

-The sample is vaporised in the presense of gaseous solvents

-It is passed down a lon tube lined with an absorbing agent.

-Each substance dissolves differently in the gas and stays there for a unique, specific time - retention time.

-Eventually, the substance leaes the gas and is absorbed by the lining

-It is then analysed to make a chromatogram

-Standard samples of drugs and urine samples are run so drugs can be identified and quantified in the chromtogram.

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Autotrophs- organisms that use light or chemical energy and inorganic molecules to synthesis complex organic molecules.

Heterotrophs- Organisms that ingest and digest complex organic molecules releasing the chemical potential energy stored in them.

Light energy is used in photosynthesis to produce complex organic molecules

Respiration and its dependance on photosythesis: Photo and auto can release chemical potential energy in complex organic molecules which were made during photosythesis-respiration. They use oxygen, which was first released into the atmosphere as a product of photosynthesis, for aerobic respiration. 

Photosynthesis is a two stage process that takes place in the chloroplast

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The structure of a chloroplast

The inner membrane contains transport proteins which control the entry and exit of substances between the cytoplasm and the stroma.

The grana provides a surface area for photsythetic pigments, electron carriers, and ATP sythase, all involved in the light-dependent reaction.

The photosythetic pigments are arranged into photosystems to allow for maximum absorption of light energy.

Protein embbed in the grana hold the photosystem in place.

The stroma contains enzymes needed to catalyse the reactions in the light independent stage.

The stroma surround the grana, so the products of the light independent reaction, needed in light- independent reaction, can be readil passed into the stroma.

Chloroplast can make some of the proteins they need for photsynthesis using the gentic instructions on their chloroplast DNA, and the chloroplast ribosmomes to assemble proteins.

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Photosythetic pigments

Molecules that absorb light energy. Each pigment absorbs a range of wavelengths in the visible region and has its own distinct peak of absorption. Other wavelengths are reflected.

They are substances that absorb certain wavelengths of light and reflect others. They appear to us the colour of the wavelength they reflect. There are many different pigments that act together, to capture as much light energy as possible. They are in thylakoid membranes, arranged in funnel shaped structures called photosystems, held in place by proteins 

The light-dependent stage takes place in thylakoid membranes and that the light-independent stage takes place in the stroma.  

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How light energy is converted into ATP

When a photon hits a chlorophyll molecule the energy of the photon is transferred to two electrons and they become excited. These electrons are captured by electron acceptors and passed down a series of electron carriers embedded in the thylakoid membranes. Energy is released as electrons pass down the chain of electron carriers. This pumps protons across the thylakoid membrane into the thylakoid space where they accumulate. A proton gradient is formed across the thylakoid membrane and the protons flow down their gradient, through proteins associated with ATP synthase enzymes. This flow of protons is chemiosmosis, and it produces a force which joins ADP to Pi to produce ATP. The kinetic energy from the proton flow is converted to chemical energy in the ATP molecules, which is used in the light-independent stage of photosynthesis. The making of ATP using light energy is called photophosphorylation, of which there are two types- cyclic and non cyclic. 

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How light energy is converted into ATP

Cyclic photophosphorylation:

Uses only photosystem I (P700)

The excited electrons pass to an electron acceptor and back to the chlorophyll molecule from which they were lost

No photolysis of water

No generation of reduced NADP

Small amounts of ATP formed o May be used in light-independent stage o May be used in guard cells, which contain only PS1, to bring in K+ ions, so water will follow by osmosis, causing the guard cells to swell and open the stomata.

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How light energy is converted into ATP

Non-cyclic photophosphorylation

Uses PS1 (P700), and PSII (P670).

Light strikes PSII, exciting a pair of electrons that leave the chlorophyll molecule from the primary pigment reaction centre

The electrons pass along a chain of electron carriers and the energy released is used to synthesise ATP. Light has also struck PSI, and a pair of electrons have also been lost

These electrons, along with protons (from the photolysis of water as PSII), join with NADP, which becomes reduced NADP. The electrons from PSI replace those lost at PSII

Electrons from photolysed water replace those lost by oxidised chlorophyll at PSI

Protons from photolysed water take part in chemiosmosis to make ATP and are then captured by NADP in the stroma. They will be used in the light-independent stage. 

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Light-dependent stage

Water is a source of:

Hydrogen ions to be used in chemiosmosis to produce ATP.

Electrons to replace those lost by oxidised chlorophyll.  The oxygen produced comes from water. 

CO2 diffuses into the leaf through the open stomata

CO2 combines with 5c Ribulose biphosphate, catalysed by Rubisco

This forms two molecules of glycerate 3-phosphate

GP is reduced (using Reduced NADP from the light-dependent stage) and phosphorylated (using ATP from

the light dependent stage) to form Triose Phosphate

5/6 molecules of TP are recycled by phosphorylation (using ATP from the light dependent stage) to three molecules of RuBP. 

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Light-independent Stage

Carbon dioxide is the source of carbon and oxygen for the production of all large organic molecules. 

State that TP can be used to make carbohydrates, lipids and amino acids.

State that most TP is recycled to RuBP.  

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Light-dependent stage

Water is a source of:

Hydrogen ions to be used in chemiosmosis to produce ATP.

Electrons to replace those lost by oxidised chlorophyll.  The oxygen produced comes from water. 

CO2 diffuses into the leaf through the open stomata

CO2 combines with 5c Ribulose biphosphate, catalysed by Rubisco

This forms two molecules of glycerate 3-phosphate

GP is reduced (using Reduced NADP from the light-dependent stage) and phosphorylated (using ATP from

the light dependent stage) to form Triose Phosphate

5/6 molecules of TP are recycled by phosphorylation (using ATP from the light dependent stage) to three molecules of RuBP. 

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Effect on the rate of photosynthesis

Light intensity-Affects Light-dependent directly.

• Lots of light

More excitation of electrons

So, more photophosphorylation

More ATP and reduced NADP produced

More GP reduced and phosphorylated to TP

More TP phosphorylated to RuBP

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Effect on the rate of photosythesis

• Little light

GP cannot be changed to TP

Levels of TP will fall

GP will accumulate

Less RuBP

Less CO2 fixed

Less GP formed 

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Effect on the rate of photosynthesis

Carbon Dioxide Concentration

• Lots of CO2

More CO2 fixation

More GP

More TP

More regeneration of RUBP

However, open stomata may lead to increased transpiration, so the plant may wilt if the water loss exceeds water uptake. This leads to a stress response, and following the release of abscisic acid, the stomata close, reducing the CO2 uptake, and therefore the rate of photosynthesis.

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Effect on the rate of photosynthesis

• Little CO2-affects light-independent, not dependent. 

RuBP will accumulate

Less GP

Less TP 

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Effect on the rate of photosynthesis


• High temperature

Little effect on light dependent- not dependent on enzymes except for photolysis of water.

Light-independent is a series of biochemical steps, each catalysed by a specific enzyme.

Above 25°C, photorespiration exceed photosynthesis, as the oxygenase activity of Rubisco increases more than the carboxylase activity.

ATP and reduced NADP from the light-dependent reaction are dissipated and wasted o Reduces the overall rate of photosynthesis

High temps may also denature proteins

High temp= high water loss

 This may lead to stomata closure, and the reduction of photosynthesis due to less CO2 

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Limiting factors of photsynthesis

Carbon dioxide concentrations

• Growers can increase the amounts of CO2 in their greenhouses by burning methane or oil -fired heaters.

• This will increase the rate of photosynthesis, providing that nothing else is limiting the process

Light intensity

• Light causes

Stomata to open:- CO2 can diffuse in

Trapped by Chorophyll:- Excites electrons

Splits water molecules to produce protons

• The electrons and protons are used in photophosphorylation, which produced ATP to fix CO2

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Limiting factors of photsynthesis


• The calvin cycle is very much affected by temperature as it is enzyme-catalysed. 

At too higher temperatures, the enzymes work less effectively, and O2 successfully competes for the active site of rubisco, preventing it from accepting CO2

• Also, as too higher temperatures, more water is lost from the stomata, leading to a stress response where the stomata close, limiting the availability of CO2 

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Investigating the affect on the rate of photsynthe

Could measure: 

• Volume of O₂ produced

• Rate of uptake of CO₂

• Rate of increase in dry mass of plants

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Investigating the affect on the rate of photsynthe


• using a photosynthometer/audus microburette is set up, air-tight ensuring no air bubbles are present

• gas given off by the plant over time collects in the flared end of the capillary tube

• the syringe can be used to move the air bubble into the part of the capillary tube against the scale

• distance moved by the air bubble at each light intensity can be used to work out the volume and essentially the rate (by dividing the volume by the time left)

• experiment should be repeated at the same light intensity and average values used

• apparatus should be left to acclimatise for 5 minutes

• all other factors should be kept constant for e.g. a water bath to keep the temperature constant 

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Investigating the affect on the rate of photsynthe


• cut disks from leaves

• place 5/6 in a syringe and half fill the syringe with dilute sodium hydrogencarbonate solution

• hold syringe upright placing finger over the end and gently pulling on the plunger.(air is extracted from the spongy mesophyll in the leaf disks) As density of leaf disks increases, they sink to the bottom 

• after all disks have sunk, transfer contents of syringe into a beaker. Illuminate using bright light and time how long it takes for one leaf disk to float to the top of the surface. 

• repeat at same light intensity • repeat at different light intensities

• record results in a table.

The leaves rise as they become less dense due to them photosynthesising and releasing O₂. 

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Why organisms need to respire

• Active transport- much of an organism’s energy is used for this

• Secretion- large molecules made in some cells are released by exocytosis

• Endocytosis- bulk movement of larger molecules into the cell

• Metabolic reactions- synthesis of large molecules from smaller ones- proteins from Amino Acids, steroids from cholesterol, cellulose from β-glucose. These are all anabolic

• Replication of DNA and synthesis of organelles before a cell divides

• Movement

Bacterial flagella, Eukaryotic cilia and undulipodia, Muscle contractions

• Activation of chemicals e.g. phosphorylation of glucose 

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An Adenosine group attached to a Ribose sugar and three phosphate molecules.

ATP provides the immediate source of energy for biological processes.  


Coenzymes aid in the oxidation and reduction of reactions. 

NAD combines with the Hydrogen atoms and takes them to the mitochondrial membrane where they can be later split into hydrogen ions and electrons for the election transport chain. It is used in glycolysis, the Krebs cycle and anaerobic respiration.

Coenzyme A carries acetate groups either from the link reaction, or that have been made from fatty acids or amino acids onto the Krebs cycle. 

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1. An ATP molecule is hydrolysed and the phosphate attached to the glucose molecule at C-6

2. Glucose 6 Phosphate is turned into fructose 6 phosphate

3. Another ATP is hydrolysed, and the phosphate attached to C-1

4. The hexose sugar is activated by the energy release from the hydrolysed ATP molecules. It now cannot leave the cell and is known as Hexose-1,6-biphosphate 5. It is split into two molecules of Triose phosphate

6. Two hydrogen atoms are removed from each Triose Phosphate, which involved dehydrogenase enzymes. NAD combines with the Hydrogen atoms to form reduce NAD

7. Two molecules of ATP are formed- substrate level phosphorylation

8. Four enzyme-catalysed reactions convert each triose phosphate molecule into a molecule of pyruvate. Two more molecules of ATP are formed, so there is a net gain of two ATP. 

Glycolysis occurs in the cytoplasm

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During aerobic respiration in animals, pyruvate is actively transported into mitochondria.

The Matrix:

1. Enzymes that catalyse the stages of aerobic respiration (highly-concentrated mixture of hundreds of


2.  Molecules of coenzyme NAD.

3. Oxaloacetate - the 4-carbon compound that accepts acetate from the link reaction.

4. Mitochondrial DNA, some of which codes for mitochondrial enzymes and other proteins.

5. Mitochondrial ribosomes where the proteins are assembled.

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The Inner Membrane:

6. different lipid composition than the outer layer (Impermeable to most small ions, including protons

(or else aerobic respiration would stop if damaged))

7. Is folded into many cristae to give a large surface area.

8.  Has embedded on it many electron carriers and ATP synthase enzymes.

9. high protein-to-phospholipid ratio. 

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The Outer Membrane:

10. It contains proteins, some of which form channels or carriers that allow the passage of molecules such as pyruvate.

Electron Transport Chain:

11.  Contain 100s of oxidoreductase enzymes - involved in oxidation and reduction reactions.

12. Some of the electrons carrier also has a co-enzyme that pumps (using energy released from the passage of electrons) protons from the matrix to the intermembrane space. 

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Link reaction

The link reaction takes place in the mitochondrial matrix.  

Pyruvate dehydrogenase removes hydrogen atoms from pyruvate

Pyruvate decarboxylase removes a carboxyl group, which eventually becomes CO2, from pyruvate

NAD accepts the hydrogen atoms

CoA accepts the acetate to become Acetyl CoA, which then travels to the Krebs Cycle.

That acetate is combined with coenzyme A to be carried to the next stage.  

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Krebs Cycle

1. Acetate is offloaded from CoA and joins with Oxaloacetate to form citrate.

2. Citrate is decarboxlyated and dehydrogenated to form a 5C compound.

a. The hydrogen atoms are accepted by NAD, which take them to the Electron Transport Chain b. The Carboxyl groub becomes CO2.

3. The 5C compound is decarboxylated and dehydrogenated to form a 4C compound.

4. The 4C compound is changed into another 4C compound, and a molecule of ATP is phosphorylated.

5. The second 4C compound is changed into a third 4C compound and a pair of hydrogen atoms are

removed, reducing FAD.

6. The third 4C compound is further dehydrogenated to regenerate oxaloacetate. 

During the Krebs cycle, decarboxylation and dehydrogenation occur, NAD and FAD are reduced and substrate level phosphorylation occurs.  

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Oxidative Phosphorylation

• The final stage of respiration involved electron carriers embedded in the mitochondrial membrane

• The membranes are folded into cristae, which increases the surface area for electron carriers and ATP synthase enzymes. 

• Oxidative phosphorylation is the formation of ATP by the addition of an inorganic phosphate to ADP in the presence of oxygen. 

• As protons flow through ATPsynthase, they drive the rotation part of the enzyme and join ADP to Pi to make ATP

• The electrons are passed from the final electron carrier to molecular oxygen, which is the final electron acceptor.

• Hydrogen ions also join, so oxygen is reduced to water 

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1. Reduced NAD and FAD donate hydrogens, which are split into protons and electrons, to the electron carriers.

2. The protons are pumped across the inner mitochondrial membrane using energy released from the passing of electrons down the electron transport chain.

3. This builds up a proton gradient, which is also a pH gradient, and an electrochemical gradient

4. Thus, potential energy builds up

5. The hydrogen ions cannot diffuse through the lipid part of the inner membrane, but can diffuse through ATP synthase- an ion channel in the membrane. The flow of hydrogen ions is chemiosmosis. 

Oxygen is the final electron acceptor in aerobic respiration.  

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Experimental evidence of chemiosmosis

• Researchers isolated mitochondria and treated them by placing them in a solution with a very low water potential.

• This meant that the outer membrane ruptured, releasing the contents of the intermembrane space.

• If they further treated these mitoblasts with a strong detergent, they could release the contents of the matrix.

• This allowed them to identify the enzymes in the mitochondria, and to work out that the link reaction and Krebs cycle occurred in the matrix, whilst the enzymes for the electron transfer chain were embedded in the mitochondrial membrane.

• Electron transfer in mitoblasts did not produce ATP, so they concluded that the intermembrane space was also involved

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Experimental evidence of chemiosmosis

• ATP was also not made if the mushroom-shaped parts of the stalked particles were removed from the inner membrane of the intact mitochondria.

• ATP was also not made in the presence of oligomycin, an antibiotic which is now known to block the flow of protons through the ion channel part of ATP synthase.

• In the intact mitochondria:- The potential difference across the membrane was -200mV, being more negative on the matrix side than on the intermembrane space side. The pH of the intermembrane space was lower than that of the matrix. 

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Theoretical maximum yield

The maximum yield for ATP is rarely reached as:

• Some hydrogens leak across the mitochondrial membrane

-Less protons to generate the proton motive force

• Some ATP is used to actively transport pyruvate into the mitochondria

• Some ATP is used to bring Hydrogen from reduced NAD made during glycolysis, into the cytoplasm, into the mitochondria.  

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Anaerobic respiration

Because only glycolysis occurs. The electron transport chain cannot occur, as there is no oxygen to act as the final electron acceptor. This means that the Krebs cycle stops, as there are no NAD- they are all reduced. This prevents the link reaction from occurring. Anaerobic respiration takes the pyruvate, and by reducing it, frees up the NAD, so glycolysis can continue, producing two molecules of ATP per glucose molecule respired.

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Compare and contrast anaerobic respiration


1. Pyruvate combines with a hydrogen which is provided by reduced NAD, this forms lactate and oxidised NAD

2.  it involves the enzyme lactate dehydrogenase and is refered to as the lactate pathway

3.  Oxidised NAD can go back to accepting hydrogen from glucose, and so Glycolysis can continue


1. Pyruvate is converted to ethanal which involves decarboxalation as CO2 is released. 

2. Ethanal combines with hydrogen from reduced NAD to form ethanol, catalysed by alcohol dehydrogenase

3.  Oxidised NAD can continue to go back and accept hydrogen from glucose, so glycolysis can continue 

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Respiratory Substrate

An organic substance that can be used for respiration

The higher the number of hydrogen atoms per mole, the higher the relative energy value, as more NAD molecules can be reduces & used in the Electron Transport Chain. Lipids have the most, followed by proteins, and then carbohydrates.

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