A2 Biology -unit 1

• cover the whole body
• enable cells to communicate with each other
• enable specific communication
• enable rapid communication
• enable both short term and long term responces.

- the maintenance of the internal environment in a constant state despite external changes.

Includes:

• body temp
• blood glucose conc
• water potential
• blood salt conc
• water potential
• blood pressurew
• carbon dioxide conc

Negative- The reversal of a change in the internal environment to return to a steady state or optimum position.

Positive- occours when the respose is to increase the original change.

Ectotherm- rely on EXTERNAL sources of heat to regulate its body temp

Advs- less food used in respiration so can be used in growth

Disadvs- less active in cooler temps, need sufficient stores of energy to survive the winter

Endotherm- an organisms that can use internal sources of heat, such as heat generated from metabolism in the liver, to maintain its body temperature.

Advs- a fairly constant body temp, activity when temp is cool, able to inhabit colder parts of the planet.

Disadv- energy is used to keep warm so more food required, less energy therefore used in growth

Polarised- a polarised membrane is one that has a potential difference across it. This is the resting potential.

Depolarisation- is the loss of polarisation across the membrane. It refers to the period when sodium ions are entering the cell making the inside less negative with respect to the outside.

Generator potential- is a small depolarisation caused by sodium ions entering the cell.

Receptor cells respond to changes in the environment, The gated sodium ion channels open, allowing sodium ions to diffuse across the membrane into the cell. a small chnage in potential caused by one or two sodium ion channels opening is called a generator potential. (see action potential card)

Action potential- achieved when the membrane is depolarised to a value of about +40mV. its an all-or-nothing repsonse. In the events leading up to an action potential, the membrane depolarises and reaches a threshold level, then lots of sodium ions enter the axon and an action potential is reached.

Sensory- carry the action potential from a sensory receptor to the CNS. long dendron outside CNS and a short axon.

Motor- carry and action potential from the CNS to an effector such as a muscle or gland. Cell body is in the CNS and have a long axon.

Relay- connect sensory and motor neurones

• many are long so they can transmit the action potential over a long distance
• the cell surface has many ion channels that control entry and exit of sodium and potassium or calcium ions
• they have sodium/potassium pumps that use ATP to actively transport sodium ions out of the cell and potassium ions into the cell
• they maintain the potential difference across their cell surface membrane
• They are surrounded by a fatty sheath called the myelin sheath (series of Schwann cells) that insulate tje neurone from the electrical activity from nearby cells. There are gaps in the cells called nodes of Ranvier.
• They have a cell body that contains nucleus, many mitochondria and ribsomes.

The resting potential is the potential difference or voltage across the neurone cell membrane while the neurone is at rest. It is about -60mV inside the cell compared with the outside. Other cells may also maintain a resting potential that might change under certain circumstances.

Resting neurone- when it is not transmitting an action potential. The interior is maintained as negative compared to the outside. The cell membrane is said to be polarised. (-60mV)

-channels in the cell membrane that allow the passgae of charged particles or ions. They have a mechanism called a gate which can open and close the channel. In these channels the gates respond to changes in the potential difference.

- a potential difference across the membrane of about -50mV. If the depolarisation of the membrane does not reach the threshold potential then no action potential is created. If the depolarisation reaches the threshold potential then an action potential is created. (all or nothing)

An action potential consists of a set of ionic movements.

• The membrane starts in its resting state- polarised with the inside of the cell being -60mV compared to outside
• Sodium ion channels open and some sodium ions diffuse into the cell
• The membrane depolarises- it becomes less negative with respect to the outside and reaches the threshold value of -50mV
• Voltage-gated sodium ion channels open and many sodium ions flood in. As more sodium ions enter, the cell becomes positively charged inside compared with outside.
• The potential difference across the plama membrane reaches +40mV. The inside of the cell is positive compared to the outside.
• The sodium ion channels close and potassium channels open
• Potassium ions diffuse out of the cell bringing the potential difference back to the negative inside compared with the outside- this is called repolarisation
• The potential difference overshoots slightly, making the cell hyperpolarised.
• The original potential difference is restored so that the cell returns to its resting state.

After the action potential the sodium and potassium ions are in the wrong place. The concentrations of these ions inside and outside the cell must be restored by the action of the sodium/potassium ion pumps.

For a short time after each action potential is is impossible to stimulate the cell membrane to reach another action potential. This is know as the refactory period and allows the cell to recover after an action potential. It also ensures that action potentials are only transmitted in one direction.

- the movements of ions along the neurone. The flow of ions is caused by an increase in concentration at one point, which causes diffusion away from the region of higher concentration.

The myelin sheath is an insulating layer of fatty material. Sodium and potassium ions cannot diffuse through this layer. Therefore ionic movements that create an action potential cannot occour over much ot the length of the neurone. The gaps in the shealth are called nodes of Ranvier and in myelinated neurones the action potential jumps from one node to the next speeding up the transmission of the action potential.

Neurotransmitter- a chemical that diffuses across the cleft of the synapse to transmit a signal to the postsynaptic neurone

Cholinergic synapse- those that use acetylchloline as their transmitter substance

The presynaptic neurone ends in a swelling called the synaptic knob. This knob contains a number of specilised features:

• many mitochondria
• a large amound of smooth ER
• vesicles of a chemical called acetylcholine
• voltage-gated calcium ion channels

• an action potential arrives at the synaptic knob
• the voltage-gated calcium ion channels open
• calcium ions diffuse into the synaptic knob
• the calcium ions cause the synaptic vesicles to move to and fuse with the presynaptic membrane
• acetylcholine is released by exocytosis
• acetylcholine diffuses across the cleft
• acetylcholine molecules bind to the receptor sites on the sodium ion channels in the postsynaptic membrane
• The sodium ion channels open
• Sodium ions diffuse across the postsynaptic membrane into the postsynaptic neurone
• A generator potential or excitatory postsynaptic potential is created. (EPSP)
• If sufficient generator potentials combine then the potential across the postsynaptic membrane reaches the threshold potential
• a new action potential is created by the postsynaptic neurone

Acetylcholinesterase is an enzyme found in the synaptic cleft. It hydrolyses the acetylcholine to ethanoic acid and choline. This stops the transmission of signals. The ethanoic acid and choline is recycled and they re-enter the synaptic knob and are recombined to acetylcholine using ATP.

• to connect two neurones together so that a signal is passed from one to the other
• Several neurons can coverge to one postsynaptic neurone allowing signals from different parts of the nervous system to create the same response.
• One presynaptic neurone might diverge to several postsynaptic neurones. This would allow one signal to be transmitted to several parts of the nervous system.
• Synapses ensure that signals are transmitted in the correct direction
• Synapses filter out low level signals that are unwanted
• Low level signals can be amplified by a process called summation.

-molecules that are released by endocrine glands directly into the blood. They act as messangers, carrying a signal from the endocrine gland o a specific target organ or tissue

Endocrine- a gland that secretes hormones DIRECTLY into the blood. Endocrine glands have no ducts

Exocrine- a gland that secretes molecules into a duct that carries the molecules to where they are used.

-cells that posses a specific receptor on their plasma membrane. The shape of the receptor is complementary to the shape of the hormone molecule.

Adrenaline is an amino acid derivative. The adrenaline receptor on the outside of the cell is complementary to the shape of the adrenaline molecule. The receptor is associated with an enzyme on the inner surface of the cell called adenyl cyclase. Adrenaline is called the FIRST MESSENGER (see other card). When it binds to the receptor it activates the adenyl cyclase. The adenyl cyclase converts ATP in cyclic AMP (cAMP). the cAMP is a SECOND MESSANGER inside then cell and it can then cause and effect inside the cell by activating enzyme action.

First- the hormone that trasmits a signal around the body.

Second- cAMP which transmits a signal inside the cell.

Adrenal medulla- found in the centre of the gland. The cells here manufacture and release adrenaline. Adrenaline prepares the body for activity- this includes the following effects:

• relax smooth muscle in the bronchioles
• increase stroke volume of the heart
• increase heart rate
• cause the general vasoconstriction to raise blood pressure
• stimulate conversion of glycogen to glucose
• dilate the pupils
• increase mental awareness
• inhibit the action of the gut
• causes body hair to erect

Adrenal cortex- uses cholesterol to produce certain steroid hormones. These have a variety of roles in the biody.

• The mineralocoticoids help to control the concentrations of sodium and potassium in the blood
• The glucocorticoids help to control the metabolism of carbohydrates and proteins in the liver

- a small organ that has both endocrine and exocrine functions. The majority of cells in the pancreas manufacture and release digestive enzymes (endocrine) The cells are found in small groups surrounding tiny tubules into which they secrete digestive enzymes. The tubules join to make up the pancreatic duct containing enzymes into the first part of the small intestine. The fluid contains sodium hydrogencarbonate which makes it alkaline. This helps to neutralise the contents of the digestive system that have just left the acid environemt of the stomach.

There are twi types. alpha cells manufacture and secrete the hormone glucagon. Beta cells manufacture and secrete the hormone insulin. The islets are well supplied with blood capillaries and these hormones are secreted directly into the blood. This is the endocrine function of the pancreas.

If the blood glucose concentration rises-

• It is detected by beta cells.
• Insulin is released
• Glucose is converted to glycogen

If it drops too low:

• It is detected by alpha cells
• Glucagon is released
• Conversion of glycogen to glucose

1. The cell membranes of the beta cells contain both calcium ions and potassium ion channels

2. Potassium ion channels are normally open and the calcium channels are normally closed. Potassium ions diffuse out of the cell making

Type 1- insulin dependant diabete. The body no longer is able to manufacture sufficient insulin and cannot store excess glucose as glycogen. Is treated with insulin injections

Type 2- due to specific receptors on the surface of the liver and muscle cells decline and lose their ability to respond to insulin. Can be controled by a balanced diet.Certain factors seem to bring about type 2 diabetes:

• Obesity
• a diet in high sugar
• being Asian or of Afro-caribbean origin
• family history

Control of heart rate:

• heart muscle is myogenic
• Contains its own pacemaker- the sinoatrial node (SAN).
• Supplied by nerves from the medulla oblongata of the brain.
• Heart muscle responds to adrenaline

-the removal of metabolic waste from the body.

Main substances excreted-

• Carbon dioxide as a result of respiration
• Nitrogen containing compounds such as urea (urea is from excess amino acids)

Excess carbon dioxide is toxic and a high level has 3 major effects:

• the majority of Carbon dioxide is carried in the form of hydrocarbonate ions and the formation of these also produces hydrogen ions (using carbonic anhydrase) These hydrogen ions combine with haemoglobin, and therefore compete for space with oxygen.
• The carbon dioxide also combines directly with haemoglobin to form carbaminohaemoglobin. This molecule has a lower affinity for oxygen than normal haemoglobin.
• Excess Carbon dioxide can also cause respiratory acidosis. The carbon dioxide dissolves in blood plasma. Once dissolved it can combine with water to produce carbonic acid.

CO2 + H2O -> H2CO3

The carbonic acid dissociates to form hydrogen ions:

H2CO3 -> H+  + HCO3-

The hydrogen ions lower the pH and make the blood more acidic. This is picked up by the respiratory centre in the medulla oblongata and increases breathing rate to help remove the carbon dioxide.

The body cannot store amino acids or proteins. However amino acids are transported to the liver and their toxic group is removed (deamniation). The amino group forms the very soluble, highly toxic group ammonia which is then convered into a less toxic compound called urea which is transported to the kidney to be excreted. The remaining keto acid of the amino acid can be respired or converted to a carbohydrate or fat for storage.

Deamination:

amino acid + oxygen -> keto acid + ammonia

ammonia + carbon dioxide -> urea + water

Liver cells carry out many hundreds of metabolic processes and the liver has an important role in homeostasis. It is therefore essential that is has a very good blood supply. The liver is supplied with blood from 2 sources (see below) and leaves from the hepatic vein. The liver is divided into lobes so that there is the best possible contact with the blood and the hepatocytes.

The hepatic portal vein- it is an unusual blood vessel that has capillaries at both ends- It carries deoxygenated blood from the digestive system to the liver

Hepatic artery- delieves oxygenated blood from the heart to the liver. Supplying the essential oxygen needed for many of the metabolic processes the liver carries out.

There is also a forth vessel connected to the liver- the bile duct. It carries bile from the liver to the fall bladder where it is stored until it is needed to aid fat digestion in the small intestine.

The blood from the two blood vessels in the liver mix and pass along a special chamber called a sinusoid. The sinusoid is lined by liver cells.

Kupffer cells are specialised macrophages. They move about within the sinusoids and are involved in the breakdown and recycling of old blood cells. One of the products of haemoglobin breakdown is billirubin, which is excreted as part of the bile and in faeces. Billirubin is the brown pigment in faeces.

The liver is very active and carries out a wide range of functions:

• control of blood glucose levels, amino acid levels, lipid levels.
• storage of vitamins A D and b12, iron, glycogen
• synthesis of red blood cells in the fetus, bile, plasma proteins, cholesterol
• detoxification of alcohol, drugs
• breakdown of hormones
• destruction of red blood cells.

Excess amino acids cannot be stored as the amine groups make them toxic. However the amino acid molecules contain a lot of energy. Therefore it undergoes treatment in the liver before the amino component is excreted. The treatment consists of two steps:

a) deamination

b) ornithine cycle.

the process of deamination produces ammonia which is very soluble and very toxic. This ammonia mst nor be allowed to accumilate. It also produces a keto acid whic can enter respiration directly.

Amnio acid + oxygen -> keto acid + ammonia

As ammonia is very soluble and toxic it must be converted into somthing very quickly. The ammonia is combied with carbon dioxide to produce urea. This occours in the ornithine cycle. Urea is both less soluble and less toxic than ammonia and can be passed into the blood and transported around the body to the kidney where urea is filtered out of the blood and concentrated in the urine.

Ammonia + carbon dioxide -> urea + water

- the conversion of toxic molecules into less toxic or non toxic molecules

Alcohol is a drug that depresses nerve activity. It is broken down by hepatocytes by the action of the enzyme ethanol dehydrogenase. The resulting compund is ethanal.which is dehydrogenated further. The final product is ethanoate which is combined with co-enzyme A to form acetyl coenzyme A which enters the process of respiration. The hydrogen atoms realeased during this process combine with NAD.

Most people have 2 kidneys. Each kidney is supplied with blood from the renal artery and drained via the renal vein. The role of the kidney is to remove waste products present in the blodd and to produce urine. 

In a londitudinal section of the kidney we can see that the kidney consists of easily identifiable regions surrounded by a tough capsule.

• the outer region is the cortex
• the inner region is the medulla
• In the centre is the pelvis wich leads to the ureter.

The bulk of each kidney consists of tiny tubuls called nephrons. Each nephron starts in the cortex. In the cortex the capillaries form a knot called the glomeralus. This is surrounded by a cup-shaped structure called the Bowman's capsule. Blood is pused in the Bowman's capsule but a pocess called ultrafiltration.

The capsule leads into the nephron which is divided into 4 parts:

• proximal convoluted tubule
• Loop of Henle
• distal convoluted tubule
• collecting duct

As the fluid moves along the nephron its compostion is altered. This is achieved by selective reabsorbtion. Substances are reabsored back into the tissue and blood capillaries surrounding the nephron tubule. The final product in the collecting duct is urine..

• In the proximal convoluted tubule the fluid is altered by the reabsorption of all the sugars, mostly salts and some water.
• In total about 85% of the fluid is reabsorbed here
• In tthe descending limb of the loop of Henle the water potential is decrased by the addition of salts and the removal of water.
• In the assending limb the water potential is increased as salts are removed by active transport.
• In the collecting duct hte water potential is decreased again by the removal of water. Ensuring that the urine has a low water potential. This means that the urine has a higher concentration of solutes than is found in the tissue fluid and the blood.

Blood flows into the glomerulus from the afferent arteriole. This is wider than the efferent arteriolen which carries blood away from the glomerulus. The different in diameters ensures that the blood in the capillaries of the glomerulus is under increased pressure. The pressure in the glomerulus is higher than the pressure in the Bowman's capsule. This pressure difference tends to push fluid from the blood into the Bowman's capsule.

The barrier between the blood in the capillary and the lumen of the Bowman's capsule consists of three layers:

• the endothelium of the capillary- have narrow gaps between each cell so that blood plasma and the substances dissolved in it can pass through.
• a basement membrane- consists of a fine mesh of collagen fibres and glycoproteins. These act as a filter to prevent the passage of molecules with a relative molecular mass of greater that 69000. This means that most proteins are held in the capillaries of the glomerulus
• epithelial cells of the Bowman's capsule- these are called podocytes and have a very specialised shape. Podocytes have finger-like projections called majopr processes. These ensure that there are gaps between the cells. Fluid from the blood in the glomerulus can pass between theses cells into the lumen of the Bowman's capsule.

Blood plasma containing dissolved substances is pushed under pressure from the capillary into the lumen of the Bowman's capsule. This includes the following substances:

• Water
• amino acids
• glucose
• urea
• inorganic ions (sodium, calcium, potassium)

The blood cells and proteins are left in the cappilary. The pressence of these means that the blood has a very low water potential. This low water potential means that some of the fluid is retained in the blood, and this contreains some of the wayer and dissolved substances listed above. The very low water potential of the blood is important for the reabsorbtion of the water at a later stage.

As fluid moves along the nephron, substances are removed from the fluid and reabsorbed into the blood. Most reabsorbiton occours in the proximal convoluted tubule. All the glucose and amino acids are reabsorbed here along with some water. Reabsorbtion is achieved by a combination of processes. The cells lining the proximal convoluted tubule are specialised for reabsorbtion.

• the cell surface membrane in contant with the fluid is highly folded to form microvilli  which increase the surface area,
• The membrane also contains co-transporter proteins that transport glucose or amino acids, in association with sodium ions. This is facillitated diffusion.
• The opposite membrane, close to the tissue fluid, is also folded to increase its surface area. This membrane contains sodium-potassium pumps that pump sodium ions out of the cell and potassium ions into the cell.
• The cell cytoplasm has many mitochondria. This indicates that an active process is involved as many mitochondria produces a lot of ATP.

• Sodium potassium pumps remove sodium ions from the cells lining the proximal convoluted tubule. This reduces the concentration of sodium ions in the cell cytoplasm.
• Sodium ions are transported into the cell along with glucose or amino acid molecules by facillitated diffusion
• As the glucose and amino acid concentrations rise inside the cell these substances are able to diffuse out the opposite side of the cell and into the tissue fluid. This is enhanced by the active removal of glucose and amino acids.
• From the tissue fluid these substances diffuse into the blood and are carried away.
• Reabsorbtion of salts, glucose and aminoa cids reduces the water potential in the cells and increase the water potential in the tubule fluid. This means water will enter the cells and then be reabsorbed by osmosis into the blood.
• Larger molecules such as small proteins that may have entered will be reabsorbed by endocytosis.

The loop of Henle consists of a descending limb that descends into the medulla and the assending limb that assends back out into the cortex. The arrangement of the loop of Henle allows salts to be transferred from the assending limb to the descending limb. The overall effect is to increase the concentration of salts in the surrounding medulla tissue, giving the tissue fluid in the medulla a very low water potential.

As fluid in the tubule decends deeper into the medulla its warer potential becomes lower. This is due to:

• Loss of water by osmosis into surrounding tissue fluid
• diffuision of sodium and chloride ions into the tubule from the surrounding tissue fluid.

As the fluid assends back up its water potential becomes higher:

• at the base of the tubule sodium and chloride ions diffuse out of the tubule into the tissue fluid.
• higher up the tubule sodium and chloride are actively transported into the tissue fluid
• the wall of the assending limb is impermeable
• the fluid loses salts but not water as it moves up the assending limb.

-the arrangement of the tubule in a sharp hairpin so that one part of the tubule passes close to another part with the fluid flowing in the opposite directons. This allows exhcange between the contents and can be used to create a very high concentration of solutes. The overall arrangement is to increase the efficientcy of salt transfer from the assending limb to the descending limb.

-the control and regulation of the water potential of the blood and body fluids. In himans the kidney controls the water potential of the blood.

Water is gained from:

• food
• drink
• metabolism e.g. respiration

Lost from:

• Urine
• sweat
• water vapour in exhalled air
• faeces

The walls of the collecting duct respond to the level of antidiuretic hormone (ADH) in the blood. Cells in the wall have membrane-bound receptors for ADH. When the ADh binds these receptors cause a chain of enzyme-controlled reactions inside the cell. The end result of these reactions is to insert vesicles containing water-permeable channels (aquapourins) into the cell surface membrane. This makes the walls more permeable to water. If there is more ADH in the blood, more water permeable channles are inserted. This allows more water to be reasbsorbed by osmosis into the blood. Less urine of a lowerered water potential passes out of the body. If there is less ADH the membrane folds inwards to create new vesicles that that remove the water-permeable channels from the membrane so more water passes out with the urine.

The water potential of the blood is monitored by the osmoreceptors in the hypothalumus of the brain. These cells probably respond to the effects of osmosis. When the water potential of the blood is low the osmoreceptors lose water by osmosis. This causes them to shrink and stimulate neurosecretory cells in the hypothalumus. These cells are specialised neurones that produce and release ADH. ADH is manufactured in the cell body of these cells (in the hypothalumus). ADH flows down the axon into the posterior pituitary gland where it is stored until it is needed. When the neurosecretory cells are stimulated they send action potentials down axons and this releases ADH. The ADH enters blood capillaries and is transported around the body and acts on the cells of the collecting duct. Once water potential rises less ADH is released. ADH present in blood is broken down and the collecting ducts recieve less stimulation.

-can occur for a number of reasons. The most common causes are:

• Diabetes mellitus (both type 1 and type 2 sugar diabetes)
• hypertension
• infection

Dialysis is the most common treatment for kidney failure. It removes wastes, excess fluids and dalt from blood by passing the blood over a dialysis membrane. This membrane is partially permeable and allows the exchange of substances between the blood and the dialysis fluid. This fluid contains the correct concentrations of salts, urea, water and other substances in blood plasma. Any substances in excess in the blood diffuse across the membrane. Any substances that are too low diffuse across the membrane from the dialysis fluid into the blood.

-blood is passed into a machine that contains an artificial dialysis membrane. Heparin is added to avoid clotting, and any bubbles are removed before the blood returns to the body.

-the fliter is the body's own abdominal membrane (peritoneum). First a surgeon implants a permenant tube in the abdomen. Dialysis solution is poured through the tube and fills the space between the abdominal walls and orhans. After several hours the used solution is drained from the abdomen. Patients can walk around while this type of dialysis occurs.

Advantages:

• Freedom from time consuming dialysis
• Diet is less limited
• Feeling better physically
• A better quality of life- able to travel
• no longer seeing oneself and chronically ill

Disadvatages:

• Need immunosupressant for the life of the kidney
• Need major surgery under general anaesthetic
• Ricks of surgery e.g. infection
• Frequent checks for signs of rejection
• Side effects of anti-rejection medicines.

Once implanted in the uterine lining, a human embryo starts secreting a pregnancy hormone called human chorionic gonadotrophin (hCG). hCG is a relatively small glycoprotein. Pregnancy tests are manufactured with monoclonal antibodies which are specific and only bind with hCG. When someone takes a pregnancy test a portion of the test ***** is soaked in urine. Any hCG in the urine attaches to an antibody that is tagged with a blue bead. This hCG-antibody comples moves up the ***** until it sticks to a band of immobilised antibodies. As a result all the antibodies carrying a blue bead and attached to the hCG are held in one place forming a blue line

- organisms that use light energy or chemical energy and inorganic molecules (carbon dioxide and water) to synthesise complex organic molecules.

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

• They vary is shape and size but are disc shaped between 2-10 micrometers long.
• Each chloroplast is surrounded by a double membrane-envelope
• There is an intermembranal space, about 10-20 nm wide, between the inner and outer membrane
• The outer membrane is permeable to small ions
• The inner one is less permeable and has transport proteins embedded in it, it is folded into lamellae (thin plates), which are stacked up like piles of pennies. Each stack of lamellae is called a granum (plural: grana)
• Between the grana are intergranal lamellae
• There are two distinct regions in a chloroplast- the stroma and the grana.
• The stroma is a fluid filled matrix. The reactions of the light-independant stage of photosynthesis occour here. Within the stroma are starch grains and oil droplets, as well as DNA and prokaryote-type ribosomes
• The grana are stacks of thylakoids. These are the sites of light absorbtion and ATP synthesis during the light dependant stage of photosynthesis.

• The inner membrane, with its transport proteins can control entry and exit of substances between the cytoplasm and the stroma inside the chloroplasts.
• The many gran, consisting of up to 100 thylakoid membranes, provides a large surface area for photosynthetic pigments, electron carries and ATP synthase enzymes, all of which are involved in the light dependant reaction
• The photsynthetic pigments are arranged into special structures called photosystems, which allow maximum absorbtion of light energy.
• Proteins embredded in the grana hold the photosystems in place
• The fluid-filled stroma contains the enzymes needed to catalyse the reactions of the light independat stage of photosynthesis.
• The grana are surrounded by the stroma so the products of the light-dependant reaction which are needed for the light independatn reaction can readily pass into the stroma.
• Chloroplasts can makes some the the proteins they need for photosynthesis, using genetic instructions in the chloroplast DNA, and the choloroplast ribosomes to assemble the proteins.

Chlorophyll is a mixture of pigments. All have a similar molecular structure, consisting of a long phytol (hydrocarbon) chain and a porphyrin group, which is similar to the haem group found in haemoglobin but contains magnesisum instead of iron.

• Light hitting the chlorophyll causes a pair of electrons to become associated with the magnesium to become excited.
• There are two forms of chlorophyll a- P680 and P700 and both appear yellow-green.
• Both are found ar the centre  of photosystems and are known as the primary pigment reaction centre.
• P680 is found in photosystem 2 and its peak of absorbtion is light at a wavelength of 680nm
• P700 is found in photosystem 1 and its peak of absorbtion is light at a wavelength of 700nm
• Chlorophyll a also absorbs blue light, of wavelength around 450nm
• Chlorophyll b absorbs light of wavelengths around 500nm and 640nm and appears blue-green.

Chlorophyll is a mixture of pigments. All have a similar molecular structure, consisting of a long phytol (hydrocarbon) chain and a porphyrin group, which is similar to the haem group found in haemoglobin but contains magnesisum instead of iron.

• Light hitting the chlorophyll causes a pair of electrons to become associated with the magnesium to become excited.
• There are two forms of chlorophyll a- P680 and P700 and both appear yellow-green.
• Both are found ar the centre  of photosystems and are known as the primary pigment reaction centre.
• P680 is found in photosystem 2 and its peak of absorbtion is light at a wavelength of 680nm
• P700 is found in photosystem 1 and its peak of absorbtion is light at a wavelength of 700nm
• Chlorophyll a also absorbs blue light, of wavelength around 450nm
• Chlorophyll b absorbs light of wavelengths around 500nm and 640nm and appears blue-green.

• Carotenoids reflect yellow and orange light and absorb blue light
• They do not contain a porphyrin group and are not directly involved in the light dependant reaction.
• They absorb light wavelengths that are not well absorbed by chlorophylls and pass the energy associated with that light to the chlorophyll a at base of the photosystem
• Carotene (orange) and xanthophyll (yellow) are the main carotenoid pigments

Photosystem 2 contains an enzyme that, in the pressence of light, can split water into H+ ions, electons and oxygen. This splitting of water is called photolysis. Some of the oxygen produced in this way is used by the plant for its aerobic respiration but much of it diffuses out of the leaves through stomata.

Water is a source of:

• hydrogen ions which are used in chemiosmosis to produce ATP. These protons are then accepted by a coenzyme NADP, which becomes reduced NADP, to be used during the light-independant stage to reduce carbon dioxide and produce organic molecules.
• Electrons to replace those lost by the oxidised chlorophyll.
• Water is one of the raw materials used in photosynthesis. It also keeps plant cells turgid enabling them to function. 
• The by-product of photosynthesis, oxygen, comes from water.

-the making of ATP from ADP and iP in the pressence of light.

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 along a series of electron carriers embedded in the thylakoid membranes. The electron carries are proteins that contain iron atoms. Energy is released as electrons pass along the chain of electronb carriers. This pumps protons across the thylakoid membranes and into the thylakoid space where they accumulate.A proton gradient is formed across the thylakoid membrane and protons flow down the gradient, through channels associated with ATP synthase enzymes. This flow of protons is called chemiosmosis. It produces a force that joins ADP and iP to make ATP. The kinetic energy from the proton flow is converted into chemical energy in ATP molecules, which is used in the light independant stage. The making of ATP is known as phosphorylation  and there are two types, cyclic and non cyclic.

This uses only photosystem 1 (P700). The excited electrons pass to an electron acceptor and back to the chlorophyll molecule from which they were lost. There is no photolysis of water and no generation of NADP, but small amounts of ATP are made. This may be used in the light independant reaction or it may be used in guard cells to bring in potassium ions, lowering the water potential and causing water to follow by osmosis. This causes guard cells to swell and opens stomata.

This involves both photosystem 1 and 2.

• Light strikes photosystem 2, 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 photosystem 1 and a pair of electrons are lost 
• These electrons, along with protons in the stroma (which may have diffused from the thylakoid space through ATP synthase) join NADP, which becomes reduced NADP
• The electrons from the oxidised photosystem 2 replace the electrons lost in photosystem 1
• Electrons from photolysed water replace those lost by the oxidised chlorophyll in photosystem 2.
• 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-independant stage

• Carbon dioxide from the air adiffuses into the leaf through open stomata, most which are on the underside of the leaf. It then diffuses throughout the air spaces in the spongy mesophyll and reaches the palisade mesophyll layer. Here it diffuses through the thin cellulose walls, the cell surface membrane, the cytoplasm and the chloroplast envelope, into the stroma.
• In the stroma, carbon dioxide combines with a 5-carbon compound, ribulose bisphosphate (RuBP)(a carbon dioxide acceptor). The reaction is catalysed by the enzyme Rubisco. RuBP becomes carboxylated (so it now has a carboxyl group)
• The product of this reaction is two molecules of glycerate-3-phosphate (GP). The carbon dioxide has now been fixed.
• Gp is reduced to triose phosphate (TP). ATP and reduced NADP from the light dependant reaction are used in this process.
• Five out of every six molecules of TP are recycled by phosphorylation, using ATP, from the light dependant reaction, to three molecules of RuBP.

• Some GP is used to make amino acids and fatty acids
• Pairs of TP molecules combine to form hexose sugars e.g. glucose
• Some glucose molecules may be isomerised to from other hexose sugars e.g. fructose 
• Glucose and fructose molecules may be combined to form the disaccharide sucrose-the sugar translocated in pholem sieve tubes
• Hexose sugars can be polymerised into other carbohydrates such as cellulose and starch
• TP can also be converted into glycerol and this may be combined with fatty acids formed from GP, to make lipids

-for a metabolic process is the factor that is present at the lowest of least favourable value 

The enzyme catalysed reactions of the Calvin cycle are affected by temperature. Between 0 degrees and 25 degrees the rate of photosynthesis aproximately doubles every 10 degrees rise in temperature. Above 25 degrees the rate of photosynthesis levels off as then falls as enzyme work less efficiently and as oxygen more sucessfully competes for the active site of rubisco and prevents it from accepting carbon dioxide. High temperature will also case more water loss from stomata, leading to the stress responce where the stomata close, limiting the avalibility of carbon dioxide

An increase in light intensity will alter the rate of the light dependant reaction.

• More light energy is avalible to exicte electronss
• The electrons take part in phosphorylation, so increase light intensity means that more TP and more reduced NADP will be produced.
• These are both used in the light independant stage as a source of hydrogen and energy, to reduce glycerate 3-phosphate to triose phosphate. ATP is also used to phosphorylate five our of every six molecules of TP to regenerate RuBP

If  there is little or no light avalible:

• GP cannot be changed to TP so it will accumulate and levels of TP will fall
• This will lower the amount of RUBP, reducing the fixation of carbon dioxide and the formation of more GP

• An increase in Carbon dioxide ,au ;ead to an incease in carbon dioxide fixation in the Calvin cycle.
• More carbon dioxide fixation maeans more GP hence more TP and more regeneration of RuBP
• However the number of stomata that open to allow gaseous exchange leads to increase transpiration and may lead to the plant wilting, if its wate uptake from the soil cannot exceed water loss by transpiration. This, in turn, leads to a stress responce and,following a realse of a plant growth regulator, stomata close.
• This will reduce carbon dioxid uptake and reduce rate of photosynthesis.

If carbon dioxide conc is reduced below 0.01% then RuBP will accumulate, as a result levels of GP and TP will fall.

• Increasing temperature will have little or no effect on the rate of the light-dependent reaction as, apart from photolysis of water, it is not dependant on enzymes. However it will alter the rate of the light independant reaction as that is a series of biochemical steps, each catalysed by an enzyme. Therefore increasing temperature will initially increase the rate of photosynthesis.
• However as temperatures rise above 25 degrees, the oxygenase activity of rubisco increases more than its carboxylase activity.
• This means that photorespiration exceeds photosynthesis
• As a result ATP and reduced NADP, from the light dependant reaction, are dissipated and wasted.
• This reduces the overall rate of photosynthesis
• Very high temperatures may also damage proteins involved e.g. enzymes like Rubisco
• Increased temperature causes an increase in water loss from leaves by transpiration and this may lead to closure of stomata and subsequent reduction in rate of photsynthesis.

-Anabolic reactions are biochemical reactions where larger molecules are broken down into smaller ones.

-In Catabolic reactions larger molecules are hydrolysed to produce smaller molecules

Collectively know as metabolism e.g. active transport, secretion, endocytosis ect ect

ATP is a phosphorylated nucleotide. It is the standard intermediary between energy releasing and energy consuming reactions in both prokaryote and eukaryote cells. Each molecule of consists of ADENOSINE (adenine and ribose sugar), plus three phosphate groups (more correctly phosphoryl groups) It can be hydrolysed to ADP and iP releasing 30.6kj of energy per mole. So energy is released in small, manageable amounts that wil not damage the cell or be wasted.

We say the energy is released in a quick one step hydrolysis reaction.

- an organic non-protein molecule that helps dehydrogenase enzymes to carry out oxidation reactions. Nicotamide adenine dinucleotide (NAD) is made of two linked nucleotides. It is made in the body from nicotamide (vitamin b3), the 5 carbon sugar ribose, adenine and two phosphate (phosphyll) groups. One nucleotide contains the nitrogenous base adenine. 

When a molecule of NAD has accepted two hydrogen atoms it is redued. NAD opperates during glycolysis, the link reaction and Krebs cycle and in anaerobic ethanol and lactate pathways.

- an organic non-protein molecule that helps dehydrogenase enzymes to carry out oxidation reactions. Nicotamide adenine dinucleotide (NAD) is made of two linked nucleotides. It is made in the body from nicotamide (vitamin b3), the 5 carbon sugar ribose, adenine and two phosphate (phosphyll) groups. One nucleotide contains the nitrogenous base adenine. 

When a molecule of NAD has accepted two hydrogen atoms it is redued. NAD opperates during glycolysis, the link reaction and Krebs cycle and in anaerobic ethanol and lactate pathways.

This coenzyme is made from adenosine (adenine and ribose), three phosphate (phosphyll) groups, pantothenic acid (vitamin B5) and a small cysteamine group (contains an amine group and sulphur)

-is a metabolic pathway where each glucose molecule is broken down into two molecules of pyruvate. It occours in the cytoplasm of all living cells and is common to anaerobic and aerobic respiration.

Stage 1 Phosphorylation- one ATP molecule is hydrolysed and the phosphate group is released and attaches to the glucose molecule at carbon 6. This is then changed to fructose 6 phosphate and another ATP is hydrolysed and becomes fructose 1,6, bisphosphate. This activates the hexose sugar and prevents it from leaving the cell. Note: (2 molecules of ATP for each molecule)                                                                                                   Stage 2- Splitting of hexose 1,6, bisphosphate into 2 triose phosphate                       Stage 3- Oxidation of triose phosphate- anaerobic but involves oxidation. Two hydrogen atoms are removed from triose phosphate (with dehydrogenase enzymes) These are aided but NAD which becomes reduced. Two molecules of NAD are reduced per glucose and also at this stage 2 molecules of ATP are formed (substrate level phosphorylation)                                                        Stage 4- Conversion of triose into pyruvate. Four enzyme catalysed reactions do this. Also 2 more molecules of ATP are formed. Products are: 2 ATP (net as 2 are used), 2 NAD, 2 Pyruvate

-organelles found in eukaryote cells. They are the sites of link reaction, Kreb's cycle and oxidative phosphorylation.

• All mitochondria have an inner and outer phospholipid membrane-envelope
• The outer membrne is smooth and the inner membrane is folded into cristae (sing: crista) that give the inner membrane a large surface area
• The two membranes enclose and separate two copartments within the mitochondrion. Between the inner and outer membranes the is the intermembranal space.
• The matrix is enclosed by the inner membrane. It seems semi-rigid and gel like, consisting of a mixture of proteins and lipids. It also contains looped mitochondrial DNA, mitochondrial ribosomes and enzymes

- This is where link and Kreb's cycle takes place it contains:

• Enzymes to catalyse these reactions
• molecules of coenzyme NAD
• oxaloacetate- the compound that accepts accetate drom the link reaction
• mitochondrial DNA, some of which codes for mitochondrial enzymes and proteins
• mitochondrial ribosomes

-the phospholipid composition of the outer membrane is very similar to membranes around other organelles. It contains proteins, some of which form channels or carries that allow passage of molecules such as pyruvate. Other proteins in this membrane are enzymes

The inner membrane

• Has a different compostition to the outer membrane and is impermeable to most small ions, including protons.
• It is folded into many cristae to give a large surface area
• Has embedded into it many electron carries and ATP synthase enzymes
• Each electron carries is an enzyme each associated with a non-protein group (cofactor)
• These cofactors can accept and donate electrons
• They are oxidoreductase enzymes are they are involved in oxidation and reduction reactions.
• Some of the electron carries also have a coenzyme which pumps protons from the matrix into the intermembranal space.
• Because the inner membrane is impermeable to small ions protons accumulate in the intermembranal space. As a result this space has a lower pH.

-the flow of protons down a proton gradient. (in the case of respiration through ATP synthase enzymes)

-converts pyruvate into acetate. NAD is reduced.

• Pyruvate dehydrogenase removes hydrogen atoms from pyruvate,
• Pyruvate hydrogenase also removes the carboxyll group, which eventually becomes carbon dioxide from pyruvate.
• The coenzyme NAD accpets the hydrogen atoms
• Coenzyme A accepts acetate to become acetyl coenzyme A. The function of CoA is to carry acetate into Kreb's cycle. 
• Note: No ATP is produced. However each NAD will take a pair of hydrogen atoms to the inner mitochondrial membrane and they will be used to make ATP during oxidative phosphorylation.

-oxidises acetate to carbon dioxide. NAD and FAD are reduced. ATP is made by substrate level phosphorylation.

• Takes place in the mitochondrial matrix.It produces one molecule of ATP and three NAD and 1 FAD and these coenzymes have the potential to make more ATP during oxidative phosphorylation.
• The acetate from acetyl coenzyme A joins with oxaloacetate to form citric acid. Coenzyme A is released so it becomes avalible to collect more acetate.
• Citrate is decarboxyilated to form a 5carbon compound and NAD becomes reduced.
• This is the decarboxylated and dehydrogenate to form a 4C compounr and another molecule of NAD is reduced.
• The 4C compound is changed into another 4C compound and another pair of hydrogen atoms are removed but this time accepted by FAD
• The third 4C compound is further dehydrogenated and regenerates the oxaloacetate and another molecule of NAD is reduced.
• Note there are 2 turns of the cycle per glucose.

-is the formation of ATP by adding a phosphate group to ADP, in the pressence of oxygen which is the final electron acceptor.

• As protons flow through and ATP synthase enzyme, they drive the rotation of part of the enzyme and join ADP and iP to form ATP
• The electrons are passed from the last electron carrier in the chain to molecular oxygen, which is the final electron acceptor
• Hydrogen ions also join so that oxygen is reduced to water
• Reduced NAD and FAD will provide electrons to the electron transport chain, to be used in oxidative phosphorylation
• Reduced NAD also provides hydrogen ions that contribute to the build ip of the proton gradient for chemiosmosis. The hydrogens from reduced FAD stay in the matrix but can combine with oxygen to form water.
• Together with the ATP made during glycolysis and Kreb's cycle, the total yield of ATP per molecule of glucose respired should be about 30.

About 30 molecules of ATP should be produced per molecule of glucose. However this is rarely achieved:

• Some protons leak across the mitochondrial membrane, reducing the number of protons to generate the proton motive force.
• Some ATP produced is used to actively transport pyruvate into the mitochondria
• Some ATP is used for the shuttle to bring hydrogen from reduced NAD made during glycolysis, in the cytoplasm, into the mitochondria

-occours in mammalian muscle tisse during vigorus exercise, when the demand for ATP is high and there is an oxygen deficit

• Reduced NAD much be reoxided
• Pyruvate is the hydrogen acceptor
• it accepts hydrogen atoms from reduced NAD
• NAD is now reoxidised and is avaliable to accept more hydrogen atoms from glucose.
• Glycolysis can not continue, generating enough ATP to sustain muscle contraction
• The enzyme lactate dehydrogenase catalyses the oxidation of reduced NAD, together with the reduction of pyruvate to lactate. 
• The lactate can be converted back into pyruvate in the liver.

Under anaerobic conditions in yeast cells.

• each pyruvate molecule loses a carbon dioxide molecule; it is decarboxylated and become ethanal.
• this reaction is catalysed by the enzyme pyruvate decarboxylase which has a coenzyme bound to it
• ethanal accepts hydrogen atoms from reduced NAD, which becomes reoxidsed as ethanal is reduced to ethanol
• the reoxidised NAD can now accept more hydrogen atoms from glucose, during glycolysis

-an organic substance that can be used for respiration

Carbohydrates are mainly used.

Proteins are only used when an organism undergoes fasting

Lipids contain the most energy but only the glycerol can be respired, fatty acids cannot, but these produce a lot of ATP